WO2009124333A1 - Modified chaperonin 10 and prr signaling - Google Patents

Modified chaperonin 10 and prr signaling Download PDF

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Publication number
WO2009124333A1
WO2009124333A1 PCT/AU2008/000520 AU2008000520W WO2009124333A1 WO 2009124333 A1 WO2009124333 A1 WO 2009124333A1 AU 2008000520 W AU2008000520 W AU 2008000520W WO 2009124333 A1 WO2009124333 A1 WO 2009124333A1
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WIPO (PCT)
Prior art keywords
polypeptide
cpn10
nucleic acid
group
amino acid
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PCT/AU2008/000520
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French (fr)
Inventor
Dean Jason Naylor
Richard J. Brown
Christopher Bruce Howard
Christopher J. De Bakker
Linda Allison Ward
Jeanette Stok
Walter Van Heumen
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Cbio Limited
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Priority to PCT/AU2008/000520 priority Critical patent/WO2009124333A1/en
Priority to EP20090730646 priority patent/EP2265635A4/en
Priority to US12/934,980 priority patent/US9234019B2/en
Priority to JP2011503310A priority patent/JP2011519548A/en
Priority to CN200980112775.5A priority patent/CN102015757B/en
Priority to RU2010145972/10A priority patent/RU2010145972A/en
Priority to PCT/AU2009/000444 priority patent/WO2009124353A1/en
Priority to BRPI0911676A priority patent/BRPI0911676A2/en
Priority to MX2010011169A priority patent/MX2010011169A/en
Priority to KR1020107025213A priority patent/KR20110005710A/en
Priority to CA2720617A priority patent/CA2720617A1/en
Priority to NZ588467A priority patent/NZ588467A/en
Priority to AU2009235953A priority patent/AU2009235953B2/en
Publication of WO2009124333A1 publication Critical patent/WO2009124333A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4715—Pregnancy proteins, e.g. placenta proteins, alpha-feto-protein, pregnancy specific beta glycoprotein
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6863—Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701—Details
    • G01N2333/471—Pregnancy proteins, e.g. placenta proteins, alpha-feto-protein, pregnancy specific beta glycoprotein
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value

Definitions

  • the present invention relates to modified chaperonin 10 polypeptides, and to nucleic acids encoding the same.
  • the present invention further relates to mutants of chaperonin 10 and to compositions comprising such polypeptides.
  • Cpn10 Mammalian chaperonin 10
  • Hsp10 heat shock protein 10
  • EPF early pregnancy factor
  • Cpn60 mitochondrial 'molecular chaperone' protein involved in protein folding together with chaperonin 60 (Cpn60), also known as heat shock protein 60 (Hsp60).
  • Cpn10 and Cpn60 are homologues of the bacterial proteins GroES and GroEL respectively.
  • GroES and Cpn10 each oligomerise into seven member rings that bind as a lid onto a barrel-like structure comprising fourteen GroEL or seven Cpn60 molecules respectively, which tether denatured proteins to the complex (Bukau and Horwich, 1998, Cell 92:351-366; Hartl and Hayer-Hartl, 2002, Science 295:1852-1858).
  • Cpn10 proteins are highly conserved across species. Human Cpn10 is 100% identical to bovine, canine, ovine and porcine Cpn10 and differs from rat Cpn10 at only a single amino acid position.
  • each monomer is comprised of essentially three different structural regions, a core anti-parallel ⁇ -barrel region flanked by a "roof ⁇ -hairpin loop region and a "mobile loop” region.
  • the anti-parallel ⁇ - barrel region of each monomer forms the core of a dome and when assembled in the heptamer the ⁇ -hairpin loops of each monomer form the roof of the dome.
  • the mobile loop region is at the opposite end of the ⁇ -barrel to the roof loops.
  • a section of the anti-parallel ⁇ -barrel region forms an inward facing lower rim region of the cavity. This lower rim region contains a number of phylogenetically conserved amino acids including a Tyrosine at position 75 (Y75).
  • Cpn10 In addition to its intracellular role as a molecular chaperone, Cpn10 is also frequently found at the cell surface (see Belles etai, 1999, Infect lmmun 67:4191-4200) and in the extracellular fluid (see Shin et al., 2003, J Biol Chem 278:7607-7616) and is increasingly being recognised as a regulator of the immune response. However the sites within the Cpn10 molecule responsible for mediating this immunomodulatory activity have remained elusive.
  • the present invention relates to the discovery that modification of Cpn10 affects the immunomodulatory activity of Cpn10, in particular its role in binding ligands of pattern recognition receptors (PRRs) such as Toll-like Receptors (TLR), Nucleotide-binding domain LRR-containing family (NLR), RIG-l-like receptors (RLR), DNA-dependent activators of IRF (DAI) and C-type Lectin receptors (CLR).
  • PRRs pattern recognition receptors
  • TLR Toll-like Receptors
  • NLR Nucleotide-binding domain LRR-containing family
  • RLR RIG-l-like receptors
  • DAI DNA-dependent activators of IRF
  • CLR C-type Lectin receptors
  • the PRR may be a Toll-like Receptor (TLR), Nucleotide-binding domain LRR-containing family (NLR), RIG-l-like receptor (RLR), DNA-dependent activator of IRF (DAI) or C-type Lectin receptor (CLR).
  • TLR Toll-like Receptor
  • NLR Nucleotide-binding domain LRR-containing family
  • RLR RIG-l-like receptor
  • DAI DNA-dependent activator of IRF
  • CLR C-type Lectin receptor
  • the TLR may be selected from the group comprising of at least one of TLR3, TLR7, TLR8 or TLR9.
  • the TLR is TLR3.
  • the ligand may be an agonist or antagonist.
  • said polypeptide possesses a greater net positive charge compared to the wild-type Cpn10 polypeptide.
  • one or more wild-type Cpn10 polypeptides may form a wild-type CpniO molecule.
  • the CpIO molecule may be a heptamer molecule comprising Cpn10 polypeptide subunits.
  • the isolated polypeptide possesses at least one mutation under the dome of the wild-type Cpn10 molecule.
  • the mutation may be an amino acid substitution, addition or deletion.
  • the substitution may be the replacement of one or more amino acid residues with one or more positively charged or neutral residues or a combination thereof.
  • a negatively charged residue may be replaced with a neutral or positively charged residue.
  • a neutral residue may be replaced with a positively charged residue.
  • the positively charged residue may be arginine (R), lysine (K) or histidine (H).
  • the neutral residue may be asparagine (N), glutamine (Q), serine (S), threonine (T), glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), tyrosine (Y), tryptophan (W), cysteine (C), methionine (M) or H (above pH 6.04).
  • the mutation under the dome may be a mutation in either the mobile loop, or the roof loop, or at a position wherein the residue has free side chains within the inner surface of the Cpn10 molecule, or a combination thereof.
  • the polypeptide comprises a mutation at an amino acid position selected from the group consisting of position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41, 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, and 96 of the wild-type Cpn10 molecule or a combination thereof.
  • said polypeptide comprises a mutation selected from the group consisting of F12K, D13K, A21K, A22K, E23K, T24K, V25K, T26K, G28K, G29K, I30K, M31K, L32K, P33K, E34K, S36K, Q37K, G38K, V40K, L41K, S52K, G54K, G56K, G57K, E58K, I59K, Q60K, P61K, V62K, E74K, Y75K, G76K, G77K, T78K, V81K, D84K, D86K, F88K, L89K, D92K, G93K, D94K, L96K, F12R, D13R, A21R, A22R, E23R, T24R, V25R, T26R, G28R, G29R, I30R, M31R, L32R, P33R, E34K, S36K, Q37
  • the polypeptide may comprise two or more mutations.
  • the polypeptide may comprise mutations selected from the group comprising E74K,Y75E; Y75G,G76K; Y75K,D94K and E34Q,Y75K.
  • the polypeptide may lack, or substantially lack, the N-terminus, the mobile loop, the ⁇ -hairpin roof loop or a combination thereof.
  • the polypeptide may be selected from the group consisting of Cpn10- ⁇ Nterm-Y75K, X-Cpn10- ⁇ ml-Y75K and Cpn10- ⁇ - barrel-Y75K.
  • the polypeptide may comprise an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58 and 61-102.
  • the polypeptide may comprise mutations selected from the group consisting of Y75K, Y75R, (Y75G,G76K), Y75GK, D94K, D94N, (Y75K,D94K) and (E34Q,Y75K).
  • the polypeptide may comprise an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 31, 37, 43, 49, 52 and 55.
  • the polypeptide may be naturally-derived, recombinantly produced or synthetically produced.
  • the Cpn10 may be of eukaryotic origin.
  • the polypeptide may be of mammalian origin.
  • the polypeptide may be human Cpn10.
  • an isolated nucleic acid encoding a polypeptide according to the first aspect.
  • the isolated nucleic acid may comprise a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 17-18, 20-21, 23-24, 26-27, 29-30, 32-33, 35-36, 38-39, 41-42, 44-45, 47-48, 50-51, 53-54, 56-57 and 59-60.
  • the isolated nucleic acid may comprise a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 32-33, 35-36, 50-51, 53-54 and 56-57.
  • an expression construct comprising a nucleic acid according to the second aspect operably-linked to one or more regulatory sequences.
  • the nucleic acid may be a codon optimised Cpn10 nucleic acid.
  • the codon optimised nucleic acid sequence may have one or more nucleotide substitutions that increase the utilisation of transfer RNA pools, exploit more efficient stop codons, remove RNA secondary structures and/or destabilising elements.
  • a host cell expressing a polypeptide of the first aspect, or comprising a nucleic acid of the second aspect or an expression construct of the third aspect.
  • an antibody that selectively binds to a polypeptide of the first aspect.
  • a pharmaceutical composition comprising a polypeptide of the first aspect, a nucleic acid of the second aspect or an expression construct of the third aspect or an antibody of the fifth aspect.
  • a method of treating a subject including the step of administering to said subject a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
  • the treatment may modulate the immune response in the subject.
  • the immune response may be modulated via regulation of PRR signalling.
  • a method for treating or preventing a disease, disorder or condition in a subject comprising administering to the subject an effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
  • the disease, disorder or condition may be selected from acute or chronic inflammatory diseases such as, insulin dependent diabetes mellitus, systemic lupus erythematosis, Sjorgren's disease, Graves disease, multiple sclerosis, rheumatoid arthritis, chronic fatigue syndrome, Alzheimer's disease, asthma, allergy, multiple sclerosis, GVHD, artherosclerosis, inflammatory pain or an infectious disease.
  • the infectious disease may result from a bacterial, viral, or fungal infection.
  • a ninth aspect of the present invention there is provided a method for modulating PRR signalling in a subject, or in at least one cell, tissue or organ thereof, the method comprising administering a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
  • a method for modulating the production and/or secretion of one or more immunomodulators in a subject, or at least one cell, tissue or organ thereof comprising administering a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
  • the polypeptide may modulate signalling from a PRR by binding a PRR ligand.
  • the immunomodulator may be a pro-inflammatory cytokine or chemokine or an anti-inflammatory cytokine or chemokine.
  • the cytokine or chemokine may be selected from TNF- ⁇ , IL-1 , IL-6, RANTES, IL-10, TGF- ⁇ or a type I interferon.
  • the type I interferon may be IFN ⁇ or IFN ⁇ .
  • an eleventh aspect of the present invention there is provided a method for inhibiting the production and/or secretion of one or more immunomodulators in a subject, or at least one cell, tissue or organ thereof, the method comprising administering an effective amount of a Cpn 10 polypeptide of the first aspect or a nucleic acid of the second aspect.
  • the polypeptide may modulate signalling from a PRR by binding a PRR ligand.
  • the immunomodulator may be a pro-inflammatory cytokine or chemokine or an antiinflammatory cytokine or chemokine.
  • the cytokine or chemokine may be selected from TNF- ⁇ , IL-1 , IL-6, RANTES, IL-10, TGF- ⁇ or a type I interferon.
  • the type I interferon may be IFN ⁇ or IFN ⁇ .
  • the assay for the formation of a complex may be a competitive binding assay, a two-hybrid assay, an electrophoretic mobility shift (gel-shift) assay and/or a plate capture assay.
  • the assay may be qualitative or quantitative. According to a thirteenth aspect of the present invention there is provided a method of screening for a compound that modulates the activity of a polypeptide of the first aspect, the method comprising the steps of:
  • Assaying for activity of the polypeptide may comprise a step of adding a labelled substrate and measuring a change in the labelled substrate.
  • a fourteenth aspect of the present invention there is provided a method of screening for a PRR ligand, the method comprising the steps of:
  • PRR ligand compound and the polypeptide of the first aspect.
  • the invention also contemplates variants, derivatives, homologues, analogues and fragments of the isolated Cpn10 polypeptides and polynucleotides according to the above aspects and embodiments.
  • the Cpn 10 polypeptides and polynucleotides may be derived from any animal, may be generated using recombinant DNA technologies or may be synthetically produced.
  • Cpn10 may be a eukaryotic Cpn10.
  • Cpn10 is human Cpn10.
  • the wild-type Cpn10 molecule or polypeptide may be acetyl-Cpn10 (SEQ ID No. 1) or X- Cpn10 (SEQ ID No. 6).
  • the immunomodulatory activity of a Cpn 10 polypeptide may involve generation of heptamers of the polypeptide.
  • wild-type as used herein in relation to Cpn 10 molecules or polypeptides includes native or non-native forms.
  • native human Cpn 10 is acetylated at its N-terminus.
  • the present invention contemplates, within the scope of the term wild-type, acetylated or non-acetylated Cpn10 molecules.
  • the wild-type Cpn10 molecule may be acetyl-Cpn10 or X-Cpn10 as represented by SEQ ID Nos. 1 or 6 respectively.
  • immunomodulator means a molecular mediator which interacts with the immune system and that plays a role in the activation, inhibition, modulation, maintenance, maturation, suppression or augmentation of an immune response.
  • PRRs protein-specific proliferative receptors
  • TLRs Toll-like receptors
  • NLRs Nucleotide-binding domain LRR-containing family
  • RLRs RIG-l-like receptors
  • DAIs DNA-dependent activators of IRF
  • CLRs C-type Lectin receptosr
  • TLRs means receptors which interact with pathogens and initiate the host immune response to infection.
  • activation of TLRs by pathogens sets in motion an innate immune inflammatory process that prevents pathogen dissemination and, through TLRs on dendritic cells, directs the development of acquired immunity.
  • the TLRs are encoded by a limited number of genes in the germline, 10 known in humans. These 10 receptors recognize a wide variety of pathogen-derived molecular signatures, including glycolipids such as lipopolysaccharide, proteins such as flagellin, and nucleic acids such as dsRNA.
  • TLRs can be divided into two groups, cell surface TLRs which generally recognize hydrophobic ligands and intracellular TLRs (i.e. TLR-3, TLR-7, TLR-8 and TLR-9) which generally recognize nucleic acid based ligands.
  • modulating refers to increasing or decreasing the level of activity, production, secretion or functioning of a molecule in the presence of a particular modulatory molecule or agent of the invention compared to the level of activity, production, secretion or other functioning thereof in the absence of the modulatory molecule or agent. These terms do not imply quantification of the increase or decrease.
  • the modulation may be of any magnitude sufficient to produce the desired result and may be direct or indirect.
  • net charge refers to the charge of a molecule.
  • Molecules that comprise an amino acid sequence such as proteins, peptides, and polypeptides (e.g. Cpn10 polypeptide) can either be positively or negatively charged.
  • the net charge of a molecule can be calculated by subtracting the number of the acidic amino acid residues from that of the basic ones.
  • net charge may be determined by its correlation to isoelectric focusing (e.g. pi as shown in Example 2) which takes place in a pH gradient and is produced by an electric field. Before an electric field is applied the gel has a uniform pH-value and almost all the carrier molecules are charged.
  • the negatively charged molecules move towards the anode, the positively charged ones to the cathode.
  • the molecules align themselves in between the cathode and the anode at a pH environment where they have a net neutral charge (i.e. at their pl- value).
  • net positive charge is the overall charge of a molecule wherein the number of basic amino acid residues are greater than the number of acidic ones in the molecule and/or the molecule's migration to the cathode when applied to electric field within a molecular technique such as isoelectric focusing.
  • under the dome means the inner surface of the dome of the
  • Cpn10 molecule which is located inside the heptameric ring of identical 10 kDa Cpn10 subunits ( Figure 1).
  • the regions of Cpn10 molecule that are under the dome include the mobile loop and the roof loop which protrude from an irregular ⁇ -barrel topology of each Cpn10 subunit, the lower rim region and any residue that has free side chains within the inner surface of the molecule such as
  • L96 (residue numbering is based on either X-Cpn10 (SEQ ID No. 6) or acetyl-Cpn10 (SEQ ID No. 1 ) as described herein).
  • mobile loop is a flexible region of the Cpn10 molecule that comprises 18 amino acid residues.
  • the mobile loop comprises residues A21 to G38 (see Figure 1; residue numbering is based on either X-Cpn10 (SEQ ID No.6) or acetyl-Cpn10 (SEQ ID No. 1) as described herein).
  • roof loop is a flexible region of the Cpn10 molecule that comprises 14 amino acid residues.
  • the roof loop comprises residues S52 to V62 (see Figure 1 ; residue numbering is based on either X-Cpn10 (SEQ ID No. 6) oracetyl-Cpn10 (SEQ ID No. 1) as described herein).
  • lower rim region as used herein means the collection of amino acids surrounding Tyrosine (Y) 75 of human Cpn10 (or its equivalent in other homologues).
  • the lower rim region comprises at least the amino acid residues Glutamic Acid (E) 74,Tyrosine (Y) 75, and Glycine (G) 76 of human Cpn10 (or its equivalent in other homologues).
  • amino acid as used herein means any molecule that contains both amine and carboxyl functional groups.
  • charged residue means any amino acid residue with a side-chain that has the potential to carry a positive or negative charge.
  • polypeptide means a polymer made up of amino acids linked together by peptide bonds.
  • polypeptide may constitute a portion of a full length protein.
  • polypeptide refers to a polypeptide that may exhibit at least one modification of its amino acid sequence, compared to a wild type Cpn10 molecule.
  • the modification may include chemical modifications such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which are naturally occurring in human proteins.
  • chemical modifications such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which are naturally occurring in human proteins.
  • polynucleotide refers to a single- or double- stranded polymer of deoxyribonucleotide, ribonucleotide bases or known analogues of natural nucleotides, or mixtures thereof. The term includes reference to the specified sequence as well as to the sequence complimentary thereto, unless otherwise indicated.
  • polynucleotide and nucleic acid are used interchangeably herein.
  • isolated means that the molecule in question has been removed from its natural environment or host, and associated impurities reduced or eliminated such that the molecule in question is the predominant species present (e.g., on a molar basis it is more abundant than any other individual species in the composition/sample).
  • a substantially purified fraction is a composition wherein the object species comprises at least about 30 percent of all macromolecular species present.
  • a substantially pure composition will comprise more than about 80 to 90 percent of all macromolecular species present in the composition.
  • the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
  • the term "substantially” means the majority but not necessarily all, and thus in relation to a modified polypeptide "substantially” lacking a component region of a corresponding wild-type polypeptide, the modified polypeptide may retain a portion of that component region.
  • a modified polypeptide "substantially” lacking a component region of a corresponding wild-type polypeptide may retain approximately 50 percent or less of the sequence of the component region, although typically the component region is rendered structurally and/or functionally inactive by virtue of the proportion of the sequences of the region omitted.
  • conservative amino acid substitution refers to the replacement of one amino acid with another amino acid having similar structural and/or chemical properties. Conservative amino acid substitutions may be made on the basis of similarity in one or more of the following: polarity, charge, solubility, hydrophobic ⁇ , hydrophilicity, and/or the amphipathic nature of the residues involved.
  • nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tyrosine, tryptophan, cysteine and methionine; polar uncharged amino acids include glycine, serine, threonine, asparagine, and glutamine; polar positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
  • Amino acid "Insertions" or “deletions” are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids.
  • the variation may be experimentally determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity.
  • treatment refers to any and all uses which remedy a disease state or symptoms, prevent the establishment of disease, or otherwise prevent, hinder, retard, or reverse the progression of disease or other undesirable symptoms in any way whatsoever.
  • the term "effective amount” includes within its meaning a non-toxic but sufficient amount of an agent or compound to provide the desired therapeutic or prophylactic effect. The exact amount required will vary from subject to subject depending on factors such as the species being treated, the age and general condition of the subject, the severity of the condition being treated, the particular agent being administered and the mode of administration and so forth. Thus, it is not possible to specify an exact "effective amount”. However, for any given case, an appropriate "effective amount” may be determined by one of ordinary skill in the art using only routine experimentation.
  • FIG. 1 A. Crystal structure of E. coli Cpn10 (GroES) showing the anti-parallel ⁇ -barrel, the roof ⁇ -hairpin loop and mobile loop regions. Cpn10 is comprised of seven identical 1OkDa subunits. The mobile loop residue G29, phylogenetically conserved aromatic residue Y71 and negatively charged residue D91 are shown.
  • GroES residues G29 (Cpn10 E34), Y71 (Cpn10 Y75) and D90 (Cpn10 D94) are shaded grey.
  • the GroES residue G29 (E34 in human Cpn10) resides in the mobile loop.
  • the phylogenetically conserved aromatic residue (Y75 in human Cpn10 and Y71 in GroES) resides under the dome on the lower rim region (comprised of the loop residues E74, Y75 and G76 in human Cpn10).
  • the GroES ribbon structure was created from the X-ray crystal coordinates published by Xu et al. (Nature 1997, 388: 741-750), in this structure the usually disordered mobile loops are perfectly aligned through interaction with GroEL (GroEL was omitted in the diagram).
  • FIG. 1 Sequence alignment of human Cpn10 with Cpn10 homologs from numerous biological kingdoms. Amino acids that are different to human Cpn10 are shaded yellow. The location of the mobile loop (blue), ⁇ -hairpin roof loop (red) and conserved tyrosine reside in the lower rim region (green; amino acid 75 in human Cpn10 and 71 in E.coli GroES) is indicated. Boxes (marked a to e) indicate the predicted boundaries of the 55 residue ⁇ -barrel core (Hunt et ai, 1997 Cell 90: 361-371). The percentage identity and similarity of the various homologs relative to human Cpn10 is shown. The SwissProt accession number of each protein is given.
  • FIG. 4 1 ⁇ g of TLR3 agonist PoIy(IrC) (a synthetic dsRNA analog) was incubated with 50 ⁇ g of a Cpn10 variant and the indicated salt concentration in 1OmM Tris-HCI (pH7.6) for 1hr at 23 0 C. Samples were resolved in a 1% TAE agarose gel and stained successively with Ethidium Bromide and Coomassie brilliant blue. Free Cpn10 migrates towards the negative electrode (top of the gel) while free poly(l:C) migrates towards the positive electrode (bottom of the gel), complexes of Cpn10-poly(l:C) retard the movement of both molecules.
  • FIG. 1 ⁇ g of human ODN-2216 class A, human ODN-2006 class B or ODN-M362 class C (TLR9 agonists; Invivogen) were incubated with 50 ⁇ g of Cpn10 in 1OmM Tris-HCI (pH7.6) and the indicated salt concentration for 15min at 23 0 C.
  • Samples were resolved in a 1% TAE agarose gel and stained with ethidium bromide. Free CpMO migrates towards the negative electrode (top of the gel) while free CpG-ODNs migrate towards the positive electrode (bottom of the gel), complexes of Cpn10-CpG-ODNs retard the movement of both molecules.
  • Cpn10 and Cpn10 mutants were formulated at I ⁇ g/ ⁇ l in formulation buffer pH7.2 (Invitrogen) and 50 ⁇ g was adsorbed to triplicate wells of a 96 well plate 16 hr at 4 0 C. Following the decanting of non-bound protein, the plate was blocked with 1% BSA and 5% sucrose in PBS pH7.2 for 2hr at 23 0 C.
  • Cpn10 modulates CpG-B ODN-induced NFKB activity.
  • RAW264.7 (mouse macrophage) cells were transfected with pNifty NF ⁇ B-luciferase reporter plasmid (InvivoGen) using Genejuice according to the manufacturers instructions (Novogen). 24 hours later cells were trypsinised, counted and 2.5 x 10 5 cells were plated in 1ml of media into each well of a 24 well plate and left to adhere overnight. 100 ⁇ g of a Cpn10 construct or Formulation buffer control was mixed with 4 ⁇ g of CpG-B ODN-1826 (Invivogen) and passed through a centrifugal filter device YM10 (Amicon).
  • FIG. 9 Effect of Cpn10 mutants on Poly (I:C) stimulation.
  • HEK293 cells were transiently transfected with plasmids encoding for TLR3 and pNifty NFkB-luciferase (InvivoGen) using GeneJuice according to the manufacturers instructions (Novogen). 24hours later the transfected cells were trypsinised, counted and 1x10 5 cells were plated in 1ml of media into each well of a 24 well plate and allowed to adhere for 24hrs. Then 100ug of Cpn10, 0.1 ug Poly (I:C) (InvivoGen) and 1OuI of SUPERase RNAse inhibitor (Ambion) were added to each well for 24hrs.
  • Human PBMC were isolated from buffy coats, counted and diluted to 3x10 6 cells/ml. 3ml of cells were plated in each well of a 6 well plate, together with 10ug Cpn10 and 0.25uM CpG-A (ODN2216, InvivoGen). Cells were incubated for 18hrs at 37 0 C 1 5% CO2, after which the supematants were removed and assayed for interferon- ⁇ levels using ELISA. Results were normalized to Ala-Cpn10 at 100%. Figure represents the mean of 3-5 replicate experiments.
  • Cpn10 is a dome-shaped, heptameric ring of identical 10 kDa subunits ( Figure 1).
  • the surface of the dome is hydrophilic and highly charged.
  • Each Cpn10 subunit forms an irregular ⁇ - barrel topology from which two large extensions protrude.
  • the first extension is a ⁇ -hairpin loop that extends towards the centre of the heptamer and forms the roof of the dome-like structure. Intriguingly, whereas the roof of GroES (E.
  • coli Cpn10 contains a cluster of negatively charged residues at the tips of the roof loops under physiological conditions, the roof of mammalian Cpn10 contains a positively charged cluster of amino acids at the tips of the roof loops; while a large portion of the roof is missing completely from the bacteriophage Cpn10 (Gp31).
  • the molecule also has another extension that is a flexible 18 amino acid mobile loop that extends from the base of the dome and mediates an interaction with Cpn60.
  • the amino acid residues in the lower rim region are phylogenetically conserved amongst most eukaryotes.
  • the inventors have generated a series of mutations through primarily amino acid substitutions which modify the net charge of a wild-type Cpn10 polypeptide and demonstrated herein that these mutations which are located under the dome are effective jn modifying the interaction of Cpn10 with one or more PRR ligands, specifically increasing the binding affinity of Cpn10 with the PRR ligand, which indicates an ability to immunomodulate the immune system/response through PRR signalling.
  • PRRs Pattern Recognition Receptors
  • TLRs Toll-like receptors
  • NLR Nucleotide- binding domain LRR-containing family
  • RLR RIG-l-like receptor
  • DAI DNA-dependent activator of IRF
  • CLR C-type Lectin receptor
  • PRRs also play a role in many inflammatory syndromes, including sepsis, autoimmune or chronic inflammatory diseases where altered self molecules hyperactivate PRRs leading to the development of a pathological state.
  • the present invention provides isolated Cpn10 polypeptides possessing an increased affinity for a PRR ligand compared to a wild-type Cpn10 polypeptide such as acetyl- Cpn10 (SEQ ID No.1) and X-Cpn10 (SEQ ID No.6). Further, the present invention provides isolated Cpn10 polypeptides possessing a greater net positive charge compared to the wild-type Cpn10 molecule based on at least one mutation under the dome of the Cpn10.
  • the type of mutation can be, but not limited to, amino acid substitution, addition or deletion in which substitution may be the replacement of a negatively charged residue with a neutral or positively charged residue or where a neutral residue is replaced with a positively charged residue.
  • the positively charged residue may be, but not limited to, arginine (R), lysine (K) or 5 histidine (H).
  • the neutral residue may be, but not limited to, asparagine (N), glutamine (Q), serine (S), threonine (T), glycine (G), alanine (A), valine (V), leucine (L) 1 isoleucine (I), proline (P), phenylalanine (F), tyrosine (Y), tryptophan (W), cysteine (C), methionine (M) and H (above pH 6.04).
  • mutations may occur at residue position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41 , 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, 96 or any combination thereof.
  • the mutation may be selected from the group comprising F12K, D13K, A21K, A22K, E23K, T24K, V25K, T26K, G28K, G29K, I30K, M31K, L32K, P33K, E34K, S36K, Q37K, G38K, V40K, L41K, S52K, G54K, G56K, G57K, E58K, I59K, Q60K, P61K, V62K, E74K, Y75K, G76K, G77K, T78K, V81K, D84K, D86K, F88K, L89K, D92K, G93K, D94K, L96K
  • the polypeptide may comprise two or more mutations.
  • the polypeptide may comprise mutations selected0 from the group comprising E74K.Y75E; Y75G.G76K; Y75K.D94K and E34Q.Y75K.
  • the polypeptide may lack, or substantially lack, the N-terminus, the mobile loop, the hairpin roof loop or a combination thereof.
  • the polypeptide may be selected from the group comprising Cpn10- ⁇ Nterm-Y75K, X-Cpn10- ⁇ ml-Y75K and Cpn10- ⁇ barrel-Y75K.
  • the polypeptide may comprise an amino acid sequence selected from the group comprising5 SEQ ID Nos. 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58 and 61-102. Furthermore, the polypeptide may comprise mutations selected from the group comprising Y75K, Y75R, (Y75G.G76K), Y75GK, D94K, D94N, (Y75K.D94K) and (E34Q.Y75K) and comprise an amino acid sequence selected from the group comprising SEQ ID Nos. 10, 13, 31, 37, 43, 49, 52 and 55.
  • the isolated Cpn10 polypeptides as described herein possess an increased affinity for PRR ligands, in particular the TLR-3 agonist poly(l:C), TLR7 and TLR8 agonist E.coli ssRNA and TLR9 agonists unmethylated CpG-oligonucleotides (ODNs) (ODN-2216 class A, ODN-2006 class B and ODN-M362 class C). It is also demonstrated herein that these Cpn10 polypeptides inhibit poly(l:C) induced NFkB activation and have an effect on interferon production in PBMCs in the presence of CpG oligonucleotides.
  • the present invention contemplates isolated Cpn10 polypeptides, herein, and its increased affinity for a PRR ligand, comprising one or more amino acid deletions, additions or substitutions in comparison with a corresponding wild-type Cpn10 polypeptide such as X-Cpn10 or acetyl-Cpn10.
  • Cpn10 may be native, naturally-derived, recombinant or synthetic Cpn10.
  • the Cpn10 molecule may be any Cpn10 polypeptide from a eukaryotic organism.
  • the Cpn10 may be derived from yeast (e.g. Saccharomyces cerevisiae), nematode (e.g. Caenorhabditis elegans), frog (e.g. Xenopus tropicalis), chicken (e.g. Gallus gall ⁇ s), zebrafish (e.g. Danio rerio), fly (e.g. fruit fly such as Drosphila melanogaste ⁇ , plant (e.g.
  • the mammalian Cpn10 may be primate, murine, ovine, bovine, canine, feline, porcine or equine. Alternatively the Cpn10 may be archaeal in origin. In particular embodiments the Cpn10 is human Cpn10.
  • the present invention relates to modifications of Cpn10 polypeptides as disclosed herein and encompasses otherwise wild-type molecules modified by the addition, deletion, or substitution of one or more amino acid residues herein, and how these modifications can increase the affinity of these Cpn10 polypeptides to a PRR ligand.
  • amino acid additions may involve the fusion of a Cpn10 polypeptide or fragment thereof with a second polypeptide or peptide, such as a polyhistidine tag, maltose binding protein fusion, glutathione S transferase fusion, green fluorescent protein fusion, or the addition of an epitope tag such as FLAG, c-myc or hexahistidine tag.
  • the Cpn10 polypeptide may or may not include the initiating methionine at the N terminus.
  • human Cpn10 may comprise at the N-terminus an additional GSM tripeptide moiety (SEQ ID No: 12; see for example WO 95/15338, the disclosure of which is incorporated herein by reference), an additional alanine (A; SEQ ID No. 3) or an additional glycine (G; SEQ ID No: 104).
  • GSM tripeptide moiety SEQ ID No: 12
  • A additional alanine
  • G additional glycine
  • polypeptides of the invention typically comprise the N-terminal sequence MAGQAFRKFL, optionally including one or more modifications as described above.
  • variant refers to substantially similar sequences. Generally, polypeptide sequence variants possess qualitative biological activity in common. Further, these polypeptide sequence variants may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity. Also included within the meaning of the term “variant” are homologues of polypeptides of the invention. A homologue is typically a polypeptide from a different species but sharing substantially the same biological function or activity as the corresponding polypeptide disclosed herein.
  • variant also includes analogues of the polypeptides of the invention, wherein the term “analogue” means a polypeptide which is a derivative of a polypeptide of the invention, which derivative comprises addition, deletion, substitution of one or more amino acids, such that the polypeptide retains substantially the same function.
  • the present invention also contemplates fragments of the polypeptides disclosed herein.
  • fragment refers to a polypeptide molecule that encodes a constituent or is a constituent of a polypeptide of the invention or variant thereof. Typically the fragment possesses qualitative biological activity in common with the polypeptide of which it is a constituent.
  • the peptide fragment may be between about 5 to about 150 amino acids in length, between about 5 to about 100 amino acids in length, between about 5 to about 50 amino acids in length, or between about 5 to about 25 amino acids in length. Alternatively, the peptide fragment may be between about 5 to about 15 amino acids in length.
  • Cpn10 polypeptides may be produced using standard techniques of recombinant DNA and molecular biology that are well known to those skilled in the art.
  • Guidance may be obtained, for example, from standard texts such as Sambrook et ai, Molecular Cloning : A Laboratory Manual, Cold Spring Harbor, New York, 1989 and Ausubel et ai, Current Protocols in Molecular Biology, Greene Publ. Assoc, and Wiley-lntersciences, 1992.
  • Cpn10 polypeptides and peptide fragments for use in accordance with the present invention may be obtained using of standard recombinant nucleic acid techniques or may be synthesized, for example using conventional liquid or solid phase synthesis techniques.
  • Cpn10 peptides may be produced by digestion of a polypeptide with one or more proteinases such as endoLys-C, endoArg- C, endoGlu-C and staphylococcus V8-protease.
  • the digested peptide fragments can be purified by, for example, high performance liquid chromatographic (HPLC) techniques.
  • Cpn10 polypeptides of the invention may be scaled-up for large-scale production purposes.
  • the present inventors have developed a bioprocess for the production of large (gram) quantities of highly pure, clinical grade Cpn10 polypeptides.
  • Cpn10 polypeptides of the present invention may also be synthesised by standard methods of liquid or solid phase chemistry well known to those of ordinary skill in the art.
  • such molecules may be synthesised following the solid phase chemistry procedures of Steward and Young (Steward, J. M. & Young, J. D., Solid Phase Peptide Synthesis. (2nd Edn.) Pierce Chemical Co., Illinois, USA (1984).
  • such a synthesis method comprises the sequential addition of one or more amino acids or suitably protected amino acids to a growing peptide chain.
  • first amino acid is protected by a suitable protecting group.
  • the protected amino acid is then either attached to an inert solid support or utilised in solution by adding the next amino acid in the sequence having the complimentary (amino or carboxyl) group suitably protected and under conditions suitable for forming the amide linkage.
  • the protecting group is then removed from this newly added amino acid residue and the next (protected) amino acid is added, and so forth. After all the desired amino acids have been linked, any remaining protecting groups, and if necessary any solid support, is removed sequentially or concurrently to produce the final polypeptide.
  • amino acid changes in Cpn10 polypeptides may be effected by techniques well known to those persons skilled in the relevant art.
  • amino acid changes may be effected by nucleotide replacement techniques which include the addition, deletion or substitution of nucleotides
  • exemplary techniques include random mutagenesis, site-directed mutagenesis, oligonucleotide-mediated or polynucleotide-mediated mutagenesis, deletion of selected region(s) through the use of existing or engineered restriction enzyme sites, and the polymerase chain reaction.
  • the generation of immunomodulatory activity by the Cpn10 polypeptides of the invention may involve the formation of heptamers of the Cpn10 polypeptides.
  • Testing of immunomodulatory activity for the purposes of the present invention may be via any one of a number of techniques known to those of skill in the art.
  • immunomodulatory activity of Cpn10 polypeptides may be determined by measuring the ability of the polypeptide to modulate signalling from the Toll-like receptor TLR-3, for example using an NF- ⁇ B-luciferase reporter cell line, and typically in the presence of a TLR-3 agonist such as poly(l:C).
  • Other TLRs such as TLR-7, 8 and 9 are also tested as described herein.
  • immunomodulatory activity may be determined using other assays in vitro, ex vivo or in vivo, for example via measurement of the production of cytokines in cells such as peripheral blood mononuclear cells, competitive binding assay, a two- hybrid assay, an electrophoretic mobility shift (gel-shift) assay or a plate capture assay.
  • cytokines in cells such as peripheral blood mononuclear cells, competitive binding assay, a two- hybrid assay, an electrophoretic mobility shift (gel-shift) assay or a plate capture assay.
  • Embodiments of the present invention provide isolated polynucleotides encoding Cpn10 polypeptides as described above, and variants and fragments of such polynucleotides.
  • Non-limiting examples of polynucleotides that are contemplated within the scope of the invention are represented herein as SEQ ID Nos. 11-12, 14-15, 17-18, 20-21, 23-24, 26-27, 29-30, 32-33, 35-36, 38-39, 41 -42, 44-45, 47-48, 50-51 , 53-54, 56-57 and 59-60.
  • polypeptides discussed above refers to substantially similar sequences.
  • polynucleotide sequence variants encode polypeptides which possess qualitative biological activity in common. Further, these polynucleotide sequence variants may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity.
  • homologues of polynucleotides of the invention are also included within the meaning of the term “variant” are homologues of polynucleotides of the invention. A homologue is typically a polynucleotide from a different species but sharing substantially the same activity.
  • Fragments of polynucleotides of the invention are also contemplated.
  • the term "fragment" refers to a nucleic acid molecule that encodes a constituent or is a constituent of a polynucleotide of the invention. Fragments of a polynucleotide, do not necessarily need to encode polypeptides which retain biological activity. Rather the fragment may, for example, be useful as a hybridization probe or PCR primer.
  • the fragment may be derived from a polynucleotide of the invention or alternatively may be synthesized by some other means, for example chemical synthesis. Polynucleotides of the invention and fragments thereof may also be used in the production of antisense molecules using techniques known to those skilled in the art.
  • the present invention contemplates oligonucleotides and fragments based on the sequences of the polynucleotides of the invention for use as primers and probes.
  • Oligonucleotides are short stretches of nucleotide residues suitable for use in nucleic acid amplification reactions such as PCR, typically being at least about 10 nucleotides to about 50 nucleotides in length, more typically about 15 to about 30 nucleotides in length.
  • Probes are nucleotide sequences of variable length, for example between about 10 nucleotides and several thousand nucleotides, for use in detection of homologous sequences, typically by hybridization.
  • the level of homology (sequence identity) between sequences will largely be determined by the stringency of hybridization conditions.
  • the nucleotide sequence used as a probe may hybridize to a homologue or other variant of a polynucleotide disclosed herein under conditions of low stringency, medium stringency or high stringency.
  • Low stringency hybridization conditions may correspond to hybridization performed at 50°C in 2 x SSC.
  • a hybridization filter may be washed twice for 30 minutes in 2 X SSC, 0.5% SDS and at least 55 0 C (low stringency), at least 60 0 C (medium stringency), at least 65°C (medium/ high stringency), at least 70°C (high stringency) or at least 75°C (very high stringency).
  • polynucleotides of the invention may be cloned into a vector.
  • the vector may be a plasmid vector, a viral vector, or any other suitable vehicle adapted for the insertion of foreign sequences, their introduction into eukaryotic cells and the expression of the introduced sequences.
  • the vector is a eukaryotic expression vector and may include expression control and processing sequences such as a promoter, an enhancer, ribosome binding sites, polyadenylation signals and transcription termination sequences.
  • Antibodies The present invention provides antibodies that selectively bind to the Cpn10 polypeptides of the present invention, as well as fragments and analogues thereof. Suitable antibodies include, but are not limited to polyclonal, monoclonal, chimeric, humanised, single chain, Fab fragments, and an Fab expression library. Antibodies of the present invention may act as agonists or antagonists of Cpn10 polypeptides, or fragments or analogues thereof. Antibodies may be prepared from discrete regions or fragments of the Cpn10 polypeptides of the invention, in particular those involved in conferring immunomodulatory activity and/or partner or substrate binding. An antigenic Cpn10 polypeptide contains at least about 5, and preferably at least about 10, amino acids.
  • an anti-Cpn10 monoclonal antibody typically containing Fab portions, may be prepared using the hybridoma technology described in Antibodies-A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor Laboratory, N.Y. (1988).
  • any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used. These include the hybridoma technique originally developed by Kohler et al., Nature, 256:495-497 (1975), as well as the trioma technique, the human B-cell hybridoma technique [Kozbor et al., Immunology Today, 4:72 (1983)], and the EBV-hybridoma technique to produce human monoclonal antibodies [Cole et al., in Monoclonal Antibodies and Cancer Therapy, pp. 77-96, Alan R. Liss, Inc., (1985)].
  • Immortal, antibody-producing cell lines can be created by techniques other than fusion, such as direct transformation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus. See, e.g., M. Schreier etal., "Hybridoma Techniques” (1980); Hammerling et al., “Monoclonal Antibodies and T-cell Hybridomas” (1981); Kennett etal., “Monoclonal Antibodies” (1980).
  • a means of producing a hybridoma from which the monoclonal antibody is produced a myeloma or other self-perpetuating cell line is fused with lymphocytes obtained from the spleen of a mammal hyperimmunised with a recognition factor-binding portion thereof, or recognition factor, or an origin-specific DNA-binding portion thereof.
  • Hybridomas producing a monoclonal antibody useful in practicing this invention are identified by their ability to immunoreact with the present recognition factor and their ability to inhibit specified transcriptional activity in target cells.
  • a monoclonal antibody useful in practicing the present invention can be produced by initiating a monoclonal hybridoma culture comprising a nutrient medium containing a hybridoma that secretes antibody molecules of the appropriate antigen specificity.
  • the culture is maintained under conditions and for a time period sufficient for the hybridoma to secrete the antibody molecules into the medium.
  • the antibody-containing medium is then collected.
  • the antibody molecules can then be further isolated by well-known techniques.
  • Cpn10 polyclonal antibody there are various procedures known in the art which may be used for the production of polyclonal antibodies to Cpn10 polypeptides of the invention, or fragments or analogues thereof.
  • various host animals can be immunized by injection with a Cpn10 polypeptide, or a fragment or analogue thereof, including but not limited to rabbits, mice, rats, sheep, goats, etc.
  • the Cpn10 polypeptide or fragment or analogue thereof can be conjugated to an immunogenic carrier, e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH).
  • BSA bovine serum albumin
  • KLH keyhole limpet hemocyanin
  • various adjuvants may be used to increase the immunological response, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminium hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parv ⁇ m.
  • Freund's complete and incomplete
  • mineral gels such as aluminium hydroxide
  • surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol
  • BCG Bacille Calmette-Guerin
  • Corynebacterium parv ⁇ m bacille Calmette-Guerin
  • Assays for immunospecific binding of antibodies may include, but are not limited to, radioimmunoassays, ELISAs (enzyme-linked immunosorbent assay), sandwich immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays, Western blots, precipitation reactions, agglutination assays, complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, and the like (see, for example, Ausubel etai, eds, 1994, Current Protocols in Molecular Biology, Vol.
  • Antibody binding may be detected by virtue of a detectable label on the primary anti-Cpn10 antibody.
  • the anti-Cpn10 antibody may be detected by virtue of its binding with a secondary antibody or reagent which is appropriately labelled.
  • a variety of methods are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
  • Antibodies of the present invention can be used in diagnostic methods and kits that are well known to those of ordinary skill in the art to detect qualitatively or quantify Cpn10 in a body fluid or tissue, or alternatively antibodies may be used in methods and compositions for the treatment of various diseases, disorders and conditions.
  • the antibody (or fragment thereof) raised against a Cpn10 polypeptide of the invention or a fragment or analogue thereof has binding affinity for Cpn10.
  • the antibody (or fragment thereof) has binding affinity or avidity greater than about 10 5 M- 1 , more preferably greater than about 10 6 M" 1 , more preferably still greater than about 10 7 M-' and most preferably greater than about 10 8 M- 1 .
  • an antibody in terms of obtaining a suitable amount of an antibody according to the present invention, one may manufacture the antibody(s) using batch fermentation with serum free medium. After fermentation the antibody may be purified via a multistep procedure incorporating chromatography and viral inactivation/removal steps. For instance, the antibody may be first separated by Protein A affinity chromatography and then treated with solvent/detergent to inactivate any lipid enveloped viruses. Further purification, typically by anion and cation exchange chromatography may be used to remove residual proteins, solvents/detergents and nucleic acids. The purified antibody may be further purified and formulated into 0.9% saline using gel filtration columns. The formulated bulk preparation may then be sterilised and viral filtered and dispensed.
  • the antibody may be purified via a multistep procedure incorporating chromatography and viral inactivation/removal steps. For instance, the antibody may be first separated by Protein A affinity chromatography and then treated with solvent/detergent to inactivate any lipid enveloped viruses. Further pur
  • an agent may be identified that is an agonist of a polypeptide of the invention or a variant or fragment thereof.
  • Agents which are agonists enhance one or more of the biological activities of the polypeptide.
  • the methods described above may identify an agent that is an antagonist of a polypeptide of the invention or a variant or fragment thereof.
  • Agents which are antagonists retard one or more of the biological activities of the polypeptide. Agonists enhance one or more of the biological activities of a molecule, such as Cpn10 polypeptides as described herein, whilst antagonists retard one or more of the biological activities of the polypeptides.
  • Such potential modulators of the activity of the polypeptides of the invention may be generated for screening by the above methods by a number of techniques known to those skilled in the art. For example, methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy may be used to model the structure of polypeptide of the invention or a variant or fragment thereof, thus facilitating the design of potential modulating agents using computer-based modeling. Various forms of combinatorial chemistry may also be used to generate putative modulators. Using the screeing methods as described below, an agent may be identified that is an agonist or antagonist of a polypeptide of the invention or a variant or fragment thereof. Antibodies, low molecular weight peptides, nucleic acids and non-proteinaceous organic molecules are examples of such agents that may act as agonists or antagonists of a polypeptide of the invention or a variant or fragment thereof.
  • Non limiting methods include the two-hybrid method, co- immunoprecipitation, affinity purification, mass spectroscopy, tandem affinity purification, phage display, label transfer, DNA microarrays/gene coexpression and protein microarrays.
  • Cpn10 polypeptides of the invention and appropriate fragments and variants can be used in high-throughput screens to assay candidate compounds for the ability to bind to, or otherwise interact with Cpn10. These candidate compounds can be further screened against functional Cpn10 to determine the effect of the compound on Cpn10 activity.
  • the polypeptides and polynucleotides of the present invention, and fragments and analogues thereof are useful for the screening and identification of compounds and agents that interact with these molecules.
  • desirable compounds are those that modulate the activity of these polypeptides and polynucleotides. Such compounds may exert a modulatory effect by activating, stimulating, increasing, inhibiting or preventing expression or activity of the polypeptides and/or polynucleotides.
  • Suitable compounds may exert their effect by virtue of either a direct (for example binding) or indirect interaction .
  • As described herein there are methods of screening for a compound that may modulate the activity of, or otherwise interact with, Cpn10 polypeptides of the invention. These compounds may be identified by a variety of suitable methods. Interaction and/or binding may be determined using standard competitive binding assays, such as gel-shift assays and plate bound assays described within, or two-hybrid assay systems.
  • the two-hybrid assay is a yeast-based genetic assay system (Fields and Song, 1989) typically used for detecting protein-protein interactions.
  • this assay takes advantage of the multi-domain nature of transcriptional activators.
  • the DNA-binding domain of a known transcriptional activator may be fused to a Cpn10 polypeptide of the invention, or fragment or variant thereof, and the activation domain of the transcriptional activator fused to a candidate protein.
  • Interaction between the candidate protein and the Cpn10 polypeptide , or fragment or variant thereof will bring the DNA-binding and activation domains of the transcriptional activator into close proximity. Interaction can thus be detected by virtue of transcription of a specific reporter gene activated by the transcriptional activator.
  • affinity chromatography may be used to identify binding partners of Cpn10.
  • a Cpn10 polypeptide of the invention, or fragment or variant thereof may be immobilised on a support (such as sepharose) and cell lysates passed over the column. Proteins binding to the immobilised Cpn10 polypeptide, fragment or variant can then be eluted from the column and identified. Initially such proteins may be identified by N-terminal amino acid sequencing for example.
  • a fusion protein may be generated by fusing a Cpn10 polypeptide, fragment or variant to a detectable tag, such as alkaline phosphatase, and using a modified form of immunoprecipitation as described by Flanagan and Leder (1990).
  • Methods for detecting compounds that modulate Cpn10 activity may involve combining a Cpn10 polypeptide with a candidate compound and a suitable labelled substrate and monitoring the effect of the compound on Cpn10 by changes in the substrate (may be determined as a function of time).
  • Suitable labelled substrates include those labelled for colourimetric, radiometric, fluorimetric or fluorescent resonance energy transfer (FRET) based methods, for example.
  • co-immunoprecipation may be used to to determine whether a candidate agent or plurality of candidate agents interacts or binds with polypeptide of the invention or a variant or 5 fragment thereof.
  • cyanotoxic organisms, cyanobacteria and/or dinoflagellates may be lysed under nondenaturing conditions suitable for the preservation of protein-protein interactions.
  • the resulting solution can then be incubated with an antibody specific for a polypeptide of the invention or a variant or fragment thereof and immunoprecipitated from the bulk solution, for example by capture with an antibody-binding protein attached to a solid support.
  • I 0 lmmunoprecipitation of the polypeptide of the invention or a variant or fragment thereof by this method facilitates the co-immunoprecipation of an agent associated with that protein.
  • identification an associated agent can be established using a number of methods known in the art, including but not limited to SDS-PAGE, western blotting, and mass spectrometry.
  • the phage display method may be used to to determine whether a candidate ⁇ 5 agent or plurality of candidate agents interacts or binds with a polypeptide of the invention or a variant or fragment thereof.
  • Phage display is a test to screen for protein interactions by integrating multiple genes from a gene bank into phage. Under this method, recombinant DNA techniques are used to express numerous genes as fusions with the coat protein of a bacteriophage such the peptide or protein product of each gene is displayed on the surface of the viral particle. A whole0 library of phage-displayed peptides or protein products of interest can be produced in this way. The resulting libraries of phage-displayed peptides or protein products may then be screened for the ability to bind a polypeptide of the invention or a variant or fragment thereof. DNA extracted from interacting phage contains the sequences of interacting proteins.
  • affinity chromatography may be used to to determine whether a candidate5 agent or plurality of candidate agents interacts or binds with a polypeptide of the invention or a variant or fragment thereof.
  • a polypeptide of the invention or a variant or fragment thereof may be immobilised on a support (such as sepharose) and cell lysates passed over the column. Proteins binding to the immobilised polypeptide of the invention or a variant or fragment thereof, may then be eluted from the column and identified, for example by N-terminal amino acid0 sequencing.
  • the present invention also contemplates compounds which may exert their modulatory effect on polypeptides of the invention by altering expression of the polypeptide.
  • such compounds may be identified by comparing the level of expression of the polypeptide in the presence of a candidate compound with the level of expression in the absence of the candidate compound.
  • Assays for immunospecific binding of antibodies may include, but are not limited to, radioimmunoassays, ELISAs (enzyme-linked immunosorbent assay), sandwich immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays, Western blots, precipitation reactions, agglutination assays, complement fixation assays, immunofluorescence assays, protein A assays, and
  • Antibody binding may be detected by virtue of a detectable label on the primary antibody.
  • the antibody may be detected by virtue of its binding with a secondary antibody or reagent which is appropriately labelled.
  • a variety of methods are known in the art for detecting binding in an immunoassay and are included in the scope of the present invention. It will be appreciated that the methods described above are merely examples of the types of methods that may be utilised to identify agents that are capable of interacting with, or modulating the activity of polypeptides of the invention or variants or fragments thereof. Other suitable methods will be known by persons skilled in the art and are within the scope of this invention.
  • compositions and routes of administration are provided.
  • Cpn10 polypeptides and polynucleotides of the invention may be useful as therapeutic agents. These molecules find use, for example, in treating or preventing a disease or condition in a subject, by administering a therapeutically effective amount of such a molecule to the subject. Typically such diseases and conditions are amenable to treatment by modulation of the immune response in the subject.
  • diseases and conditions may include acute or chronic inflammatory diseases such as insulin dependent diabetes mellitus, systemic lupus erythematosis, Sjorgren's disease, Graves disease, multiple sclerosis, rheumatoid arthritis, chronic fatigue syndrome, Alzheimer's disease, asthma, allergy, multiple sclerosis, GVHD, artherosclerosis, inflammatory pain or an infectious disease.
  • the infectious disease may result from a bacterial, viral, or fungal infection.
  • pharmaceutically useful compositions comprising Cpn10 polypeptides and polynucleotides for use in treating or preventing diseases and conditions are contemplated.
  • Agonists and antagonists of Cpn10 polypeptides of the invention may also be useful as therapeutic agents. Accordingly, the present invention also contemplates methods of treatment using such agonists and antagonists and pharmaceutical compositions comprising the same.
  • suitable compositions for use in accordance with the methods of the present invention may be prepared according to methods and procedures that are known to those of ordinary skill in the art and accordingly may include a pharmaceutically acceptable carrier, diluent and/or adjuvant.
  • compositions may be administered by standard routes.
  • the compositions may be administered by the parenteral (e.g., intravenous, intraspinal, subcutaneous or intramuscular), oral or topical route. Administration may be systemic, regional or local.
  • the particular route of administration to be used in any given circumstance will depend on a number of factors, including the nature of the condition to be treated, the severity and extent of the condition, the required dosage of the particular compound to be delivered and the potential side-effects of the compound.
  • suitable compositions may be prepared according to methods which are known to those of ordinary skill in the art and may include a pharmaceutically acceptable diluent, adjuvant and/or excipient.
  • the diluents, adjuvants and excipients must be "acceptable" in terms of being compatible with the other ingredients of the composition, and not deleterious to the recipient thereof.
  • Examples of pharmaceutically acceptable carriers or diluents are demineralised or distilled water; saline solution; vegetable based oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil, sesame oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil, sesame oil, arachis oil or coconut oil; silicone oils, including polysiloxanes, such as methyl polysiloxane, phenyl polysiloxane and methylphenyl polysolpoxane; volatile silicones; mineral oils such as liquid paraffin, soft paraffin or squalane; cellulose derivatives such as methyl cellulose, ethyl cellulose, carboxymethylcellulose, sodium carboxymethylcellulose or hydroxypropylmethylcellulose; lower alkanols, for example ethanol or iso-propanol; lower aralkanols; lower polyalkylene glycols or lower alkylene glycols, for example polyethylene glyco
  • compositions of the invention may be in a form suitable for administration by injection, in the form of a formulation suitable for oral ingestion (such as capsules, tablets, caplets, elixirs, for example), in the form of an ointment, cream or lotion suitable for topical administration, in a form suitable for delivery as an eye drop, in an aerosol form suitable for administration by inhalation, such as by intranasal inhalation or oral inhalation, in a form suitable for parenteral administration, that is, subcutaneous, intramuscular or intravenous injection.
  • a formulation suitable for oral ingestion such as capsules, tablets, caplets, elixirs, for example
  • an ointment cream or lotion suitable for topical administration
  • an eye drop in an aerosol form suitable for administration by inhalation, such as by intranasal inhalation or oral inhalation
  • parenteral administration that is, subcutaneous, intramuscular or intravenous injection.
  • non-toxic parenterally acceptable diluents or carriers can include, Ringer's solution, isotonic saline, phosphate buffered saline, ethanol and 1,2 propylene glycol.
  • suitable carriers, diluents, excipients and adjuvants for oral use include peanut oil, liquid paraffin, sodium carboxymethylcellulose, methylcellulose, sodium alginate, gum acacia, gum tragacanth, dextrose, sucrose, sorbitol, mannitol, gelatine and lecithin.
  • these oral formulations may contain suitable flavouring and colourings agents.
  • the capsules When used in capsule form the capsules may be coated with compounds such as glyceryl monostearate or glyceryl distearate which delay disintegration.
  • Adjuvants typically include emollients, emulsifiers, thickening agents, preservatives, bactericides and buffering agents.
  • Solid forms for oral administration may contain binders acceptable in human and veterinary pharmaceutical practice, sweeteners, disintegrating agents, diluents, flavourings, coating agents, preservatives, lubricants and/or time delay agents.
  • Suitable binders include gum acacia, gelatine, corn starch, gum tragacanth, sodium alginate, carboxymethylcellulose or polyethylene glycol.
  • Suitable sweeteners include sucrose, lactose, glucose, aspartame or saccharine.
  • Suitable disintegrating agents include corn starch, methylcellulose, polyvinylpyrrolidone, guar gum, xanthan gum, bentonite, alginic acid or agar.
  • Suitable diluents include lactose, sorbitol, mannitol, dextrose, kaolin, cellulose, calcium carbonate, calcium silicate or dicalcium phosphate.
  • Suitable flavouring agents include peppermint oil, oil of wintergreen, cherry, orange or raspberry flavouring.
  • Suitable coating agents include polymers or copolymers of acrylic acid and/or methacrylic acid and/or their esters, waxes, fatty alcohols, zein, shellac or gluten.
  • Suitable preservatives include sodium benzoate, vitamin E, alpha-tocopherol, ascorbic acid, methyl paraben, propyl paraben or sodium bisulphite.
  • Suitable lubricants include magnesium stearate, stearic acid, sodium oleate, sodium chloride or talc.
  • Suitable time delay agents include glyceryl monostearate or glyceryl distearate.
  • Liquid forms for oral administration may contain, in addition to the above agents, a liquid carrier.
  • suitable liquid carriers include water, oils such as olive oil, peanut oil, sesame oil, sunflower oil, safflower oil, arachis oil, coconut oil, liquid paraffin, ethylene glycol, propylene glycol, polyethylene glycol, ethanol, propanol, isopropanol, glycerol, fatty alcohols, triglycerides or mixtures thereof.
  • Suspensions for oral administration may further comprise dispersing agents and/or suspending agents.
  • Suitable suspending agents include sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethyl-cellulose, poly-vinyl-pyrrolidone, sodium alginate or acetyl alcohol.
  • Suitable dispersing agents include lecithin, polyoxyethylene esters of fatty acids such as stearic acid, polyoxyethylene sorbitol mono- or di-oleate, -stearate or -laurate, polyoxyethylene sorbitan mono- or di-oleate, -stearate or -laurate and the like.
  • the emulsions for oral administration may further comprise one or more emulsifying agents.
  • Suitable emulsifying agents include dispersing agents as exemplified above or natural gums such as guar gum, gum acacia or gum tragacanth.
  • compositions suitable for topical administration comprise an active ingredient together with one or more acceptable carriers, and optionally any other therapeutic ingredients.
  • Formulations suitable for topical administration include liquid or semi-liquid preparations suitable for penetration through the skin to the site of where treatment is required, such as liniments, lotions, creams, ointments or pastes, and drops suitable for administration to the eye, ear or nose. Drops according to the present invention may comprise sterile aqueous or oily solutions or suspensions.
  • bactericidal and/or fungicidal agents may be prepared by dissolving the active ingredient in an aqueous solution of a bactericidal and/or fungicidal agent and/or any other suitable preservative, and optionally including a surface active agent.
  • the resulting solution may then be clarified by filtration, transferred to a suitable container and sterilised. Sterilisation may be achieved by: autoclaving or maintaining at 9O 0 C-IOO 0 C for half an hour, or by filtration, followed by transfer to a container by an aseptic technique.
  • bactericidal and fungicidal agents suitable for inclusion in the drops are phenylmercuric nitrate or acetate (0.002%), benzalkonium chloride (0.01%) and chlorhexidine acetate (0.01%).
  • Suitable solvents for the preparation of an oily solution include glycerol, diluted alcohol and propylene glycol.
  • Lotions according to the present invention include those suitable for application to the skin or eye.
  • An eye lotion may comprise a sterile aqueous solution optionally containing a bactericide and may be prepared by methods similar to those described above in relation to the preparation of drops.
  • Lotions or liniments for application to the skin may also include an agent to hasten drying and to cool the skin, such as an alcohol or acetone, and/or a moisturiser such as glycerol, or oil such as castor oil or arachis oil.
  • Creams, ointments or pastes according to the present invention are semi-solid formulations of the active ingredient for external application. They may be made by mixing the active ingredient in finely-divided or powdered form, alone or in solution or suspension in an aqueous or non-aqueous fluid, with a greasy or non-greasy basis.
  • the basis may comprise hydrocarbons such as hard, soft or liquid paraffin, glycerol, beeswax, a metallic soap; a mucilage; an oil of natural origin such as almond, corn, arachis, castor or olive oil; wool fat or its derivatives, or a fatty acid such as stearic or oleic acid together with an alcohol such as propylene glycol or macrogols.
  • composition may incorporate any suitable surfactant such as an anionic, cationic or non- ionic surfactant such as sorbitan esters or polyoxyethylene derivatives thereof.
  • suitable surfactant such as an anionic, cationic or non- ionic surfactant such as sorbitan esters or polyoxyethylene derivatives thereof.
  • Suspending agents such as natural gums, cellulose derivatives or inorganic materials such as silicaceous silicas, and other ingredients such as lanolin, may also be included.
  • compositions may also be administered in the form of liposomes.
  • Liposomes are generally derived from phospholipids or other lipid substances, and are formed by mono- or multilamellar hydrated liquid crystals that are dispersed in an aqueous medium. Any non-toxic, physiologically acceptable and metabolisable lipid capable of forming liposomes can be used.
  • the compositions in liposome form may contain stabilisers, preservatives, excipients and the like.
  • the preferred lipids are the phospholipids and the phosphatidyl cholines (lecithins), both natural and synthetic.
  • compositions may be conjugated to an array of polyethylene glycol (PEG) derivatives.
  • PEG polyethylene glycol
  • PEGylation is a well established method for decreasing the plasma clearance rates of proteins, thereby increasing their efficacy (Nucci el al., 1991, Adv. Drug Del. Rev. 6:133). Additional benefits of PEGylation may include, greater stability of proteins, decreased immunogenicity, enhanced solubility and decreased susceptibility to proteolysis (Sheffield W. 2001, Curr Drug Targets Cardiovasc Haematol Disord. 1:1-22).
  • PEG molecules contain the basic repeating structure of -(OCH3CH2)n-OH and are classified into groups according to their molecular weight.
  • PEG derivatives are conjugated to proteins to increase their hydrodynamic radius and in general, their increase in half-life is directly related to the size of the PEG chain attached (Sheffield W.2001 , Curr Drug Targets Cardiovasc Haematol Disord. 1 : 1 -22).
  • compositions may also be administered in the form of microparticles.
  • Biodegradable microparticles formed from polylactide (PLA), polylactide-co-glycolide (PLGA), and epsilon- caprolactone ( ⁇ -caprolactone) have been extensively used as drug carriers to increase plasma half life and thereby prolong efficacy (R. Kumar, M., 2000, J Pharm Pharmaceut ScL 3(2) 234-258).
  • Microparticles have been formulated for the delivery of a range of drug candidates including vaccines, antibiotics, and DNA. Moreover, these formulations have been developed for various delivery routes including parenteral subcutaneous injection, intravenous injection and inhalation.
  • compositions may incorporate a controlled release matrix that is composed of sucrose acetate isobutyrate (SAIB) and organic solvent or organic solvents mixture.
  • SAIB sucrose acetate isobutyrate
  • Polymer additives may be added to the vehicle as a release modifier to further increase the viscosity and slow down the release rate.
  • SAIB is a well known food additive. It is a very hydrophobic, fully esterified sucrose derivative, at a nominal ratio of six isobutyrate to two acetate groups. As a mixed ester, SAIB does not crystallize but exists as a clear viscous liquid. Mixing SAIB with a pharmaceutically accepted organic solvent such as ethanol or benzyl alcohol decreases the viscosity of the mixture sufficiently to allow for injection.
  • An active pharmaceutical ingredient may be added to the SAIB delivery vehicle to form SAIB solution or suspension formulations.
  • the solvent diffuses from the matrix allowing the SAIB-drug or SAIB-drug-polymer mixtures to set up as an in situ forming depot.
  • compositions may be administered to subjects as compositions either therapeutically or preventively.
  • compositions are administered to a patient already suffering from a disease, in an amount sufficient to cure or at least partially arrest the disease and its complications.
  • the composition should provide a quantity of the molecule or agent sufficient to effectively treat the patient.
  • Embodiments of the invention also contemplate the administration of a polynucleotide encoding Cpn10.
  • the polynucleotide is typically operably linked to a promoter such that the appropriate polypeptide sequence is produced following administration of the polynucleotide to the subject.
  • the polynucleotide may be administered to subjects in a vector.
  • the vector may be a plasmid vector, a viral vector, or any other suitable vehicle adapted for the insertion of foreign sequences, their introduction into eukaryotic cells and the expression of the introduced sequences.
  • the vector is a eukaryotic expression vector and may include expression control and processing sequences such as a promoter, an enhancer, ribosome binding sites, polyadenylation signals and transcription termination sequences.
  • the nucleic acid construct to be administered may comprise naked DNA or may be in the form of a composition, together with one or more pharmaceutically acceptable carriers.
  • Cpn10 polypeptides of the invention may be administered alone or in conjunction with one or more additional agents.
  • a Cpn10 polypeptide of the invention may be administered together with one or more agonists capable of stimulating a TLR receptor such as TLR-3.
  • Cpn10 polypeptides of the invention contemplates combination therapy using Cpn10 polypeptides of the invention in conjunction with other therapeutic approaches to the treatment of diseases and disorders.
  • Cpn10 polypeptides may be useful in the treatment of viral diseases which are responsive to therapy with Type I interferons such as IFN ⁇ or IFN1 ⁇ and Cpn10 polypeptides of the invention may be used in conjunction with IFN ⁇ in the treatment of autoimmune diseases such as multiple sclerosis.
  • each component of the combination therapy may be administered at the same time, or sequentially in any order, or at different times, so as to provide the desired effect.
  • the components may be formulated together in a single dosage unit as a combination product. When administered separately, it may be preferred for the components to be administered by the same route of administration, although it is not necessary for this to be so.
  • the therapeutically effective dose level for any particular patient will depend upon a variety of factors including: the disorder being treated and the severity of the disorder; activity of the molecule or agent employed; the composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration; the route of administration; the rate of sequestration of the molecule or agent; the duration of the treatment; drugs used in combination or coincidental with the treatment, together with other related factors well known in medicine.
  • One skilled in the art would be able, by routine experimentation, to determine an effective, non-toxic amount of agent or compound which would be required to treat applicable diseases and conditions.
  • an effective dosage is expected to be in the range of about 0.0001 mg to about IOOOmg per kg body weight per 24 hours; typically, about 0.001 mg to about 750mg per kg body weight per 24 hours; about 0.01 mg to about 500mg per kg body weight per 24 hours; about 0.1 mg to about 500mg per kg body weight per 24 hours; about 0.1 mg to about 250mg per kg body weight per 24 hours; about 1.Omg to about 250mg per kg body weight per 24 hours.
  • an effective dose range is expected to be in the range about 1.0mg to about 200mg per kg body weight per 24 hours; about 1.0mg to about 100mg per kg body weight per 24 hours; about 1.0mg to about 50mg per kg body weight per 24 hours; about 1.0mg to about 25mg per kg body weight per 24 hours; about 5.0mg to about 50mg per kg body weight per 24 hours; about 5.0mg to about 20mg per kg body weight per 24 hours; about 5.0mg to about 15mg per kg body weight per 24 hours.
  • an effective dosage may be up to about 500mg/m 2 .
  • an effective dosage is expected to be in the range of about 25 to about 500mg/m 2 , preferably about 25 to about 350mg/m 2 , more preferably about 25 to about 300mg/m 2 , still more preferably about 25 to about 250mg/m 2 , even more preferably about 50 to about 250mg/m 2 , and still even more preferably about 75 to about 150mg/m 2 .
  • the treatment would be for the duration of the disease state.
  • the optimal quantity and spacing of individual dosages will be determined by the nature and extent of the disease state being treated, the form, route and site of administration, and the nature of the particular individual being treated. Also, such optimum conditions can be determined by conventional techniques. It will also be apparent to one of ordinary skill in the art that the optimal course of treatment, such as, the number of doses of the composition given per day for a defined number of days, can be ascertained by those skilled in the art using conventional course of treatment determination tests.
  • Cpn10-Y75K, Ala-Cpn10-Y75R and Ala-Cpn10-E34Q,Y75K was determined to be >99% by Coomassie brilliant staining on SDS-PAGE as shown in Figure 3. Aliquots were thawed once prior to use.
  • Cpn10 polypeptides which include one or more mutations such as Y75K, Y75R, Y75H, Y75D, Y75Q, (E74K,Y75E), (Y75G.G76K), Y75GK, D94K, D94N, E34Q or any combination thereof.
  • Some these Cpn10 polypeptides have an extra N-terminal Alanine (Ala) residue (e.g. Ala-Cpn10-Y75K) and/or partially or substantially lack the N-terminus, mobile loop and/or the roof loop (e.g. Cpn 10- ⁇ Nterm-Y75K, X-CpM 0- ⁇ ml-Y75K and Cpn10- ⁇ -barrel-Y75K).
  • Native bovine rhodanese (30 ⁇ M, SIGMA) was denatured in 20 mM MOPS-KOH (pH7.5), 100 mM KCI and 20 mM MgCk (buffer A) containing 5M Guanidine HCI and 8 mM DTT then subsequently diluted (75-fold) from denaturant into buffer A containing GroEL (400 nM), such that the final concentration of rhodanese was 400 nM.
  • GroEL rapidly and stably binds denatured rhodanese (D-Rho) whereas in buffer alone, D-Rho mis-folds and aggregates (ie inefficient spontaneous refolding).
  • EDTA within the rhodanese activity assay mixture chelates Mg 2+ ions, which prevents GroEL binding ATP, the result is an immediate stopping of the folding reaction. Subsequently, rhodanese activity is stopped after 6 min by the addition of 50 ⁇ L of 15% (v/v) formaldehyde (final concentration 5% v/v). Rhodanese catalyses the formation of thiocyanide ('Rhodanid') from thiosulfate and cyanide.
  • thiocyanide thiocyanide
  • Rhodanese activity measurements (150 ⁇ L) are developed by the addition of 150 ⁇ L of Ferric Nitrate reagent (164.5 mM ferric nitrate and 9.2 % v/v nitric acid). Rhodanese activity measurements are read at A450nm in 96 well microplates. A typical rhodanese folding reaction follow an exponential incline in rhodanese activity (ie folded rhodanese) with time to a maximum yield of folded rhodanese.
  • Rhodanese activity ie Cpn10 activity
  • the OnM Cpn10 standard serves as a suitable measurement of the assays' background activity; therefore the absorbance value for the OnM Cpn10 standard is subtracted from all other calculated absorbance values (or activity values).
  • the absorbance value for the 280 nM Cpn10 standard is nominated as 100% activity and all other absorbance values are converted to a relative % activity based on the 100% standard. Outlier data points are removed by comparison of duplicate measurements, >30% deviation between duplicates is considered unacceptable.
  • a linear calibration curve is generated with five standard concentrations 0 nM CpMO (0 % Activity), 140 nM Cpn10 (50 % Activity), 250 nM Cpn10 (89.3 % Activity), 280 nM Cpn10 (100 % Activity) and 350 nM Cpn10 (125 % Activity).
  • Rhodanese activity e,g, Ala-Cpn10 activity
  • Ala-Cpn10 activity is plotted against Ala-Cpn10 concentration.
  • Example 3 Cpn10 mutants bind to poly(l:C), CpG-ODNs and RNA
  • TLRs are expressed both extra- and intracellular ⁇ , those on the cell surface (TLR1, TLR2, TLR4, TLR5, TLR6, TLR10 and TLR11) generally recognize hydrophobic ligands while those in intracellular compartments (TLR3, TLR7, TLR8 and TLR9) generally recognize negatively charged nucleic acid based ligands (Akira et al. 2006, 124: 783-801 ).
  • Ala-Cpn10 binds negatively charged nucleic acid based TLR ligands, these include poly(l:C) (TLR3 agonists) as shown in Figure 4, several classes of unmethylated single-stranded CpG-oligonucleotides (ODN) as shown in Figures
  • X-Cpn10-Y75K, Ala-Cpn10-Y75K, Ala-Cpn10-Y75R, and Ala-Cpn10-D94K bind more tightly to poly(l:C) (Fig.4), CpG-ODNs (Fig. 5) and ssRNA (Fig.6) than Ala-Cpn10.
  • AIa-CpM 0- ⁇ ml-Y75K and Cpn10- ⁇ -barrel-Y75K also bind polyl:C more tightly than AIa-CpMO.
  • X-Cpn10-Y75K and AIa-CpM 0-Y75K bind so tightly toTLR3 agonist poly(l:C) that it cannot be fully released with 1M NaCI, unlike AIa-CpMO which is dissociated at 5OmM NaCI (Fig. 4).
  • X-CpMO binds the long polymers of poly(l:C) in manner that sequesters them from ethidium bromide intercalation (Fig. 4), possibly indicating that several CpMO heptamers bind a single poly(I.C) chain.
  • CpG-classes A and B bound to either X-CpM 0-Y75K or Ala-Cpn10-Y75K were mostly resistant to 50OmM NaCI (Fig. 5).
  • Ala-Cpn10 and X-Cpn10 is completely removed from ssRNA but several mutants, including X-Cpn10-Y75K and Ala-Cpn10-Y75K for example remain firmly bound in the presence of 500 mM NaCI.
  • the mutants were formulated at 10 ⁇ g/ ⁇ l in PBS pH7.2 (Invitrogen) and 50 ⁇ g was adsorbed to triplicate wells of a 96 well plate 16 hr at 4 0 C. Following the decanting of non-bound protein, the plate was blocked with 1% BSA and 5% sucrose in PBS pH7.2 for 2hr at 23 0 C.
  • RAW264.7 (mouse macrophage) cells were stably transfected with an NF ⁇ B-luciferase reporter plasmid (pNIFty2-LUC; Invivogen).
  • RAW264-pNIFty2-LUC cells were plated out and left to adhere overnight.
  • 100 ⁇ g of a Cpn10 construct or Formulation buffer control was mixed with 4 ⁇ g of CpG-B ODN-1826 (Invivogen) and passed through a centrifugal filter device YM10 (Amicon). The entire flow through volume was added to the RAW264-pNIFty2-LUC cells and incubated at 37 0 C for 5 hours.
  • CCLR 1X solution Promega luciferase lysis buffer
  • Figure 8 shows NFKB activation levels (measured by luciferase) of TLR9 when CpG-B was mixed with either a Cpn10 construct or formulation buffer.
  • the level of activation of TLR9 for AIa- Cpn10 was assigned the value of 100%.
  • Cpn10 polypeptides comprising one or more amino acid substitutions, deletions and/or additions in mobile loop (which contains amino acid residue 34), C-terminus of the ⁇ -barrel (which contains amino acid residue 94) and/or other mutants within the lower rim region bind CpG-B, such as X-Cpn10-Y75K, Ala-Cpn10-Y75K, Ala-Cpn10-D94K, Ala-Cpn10-Y75R, Ala-Cpn10-E74K,Y75E, AIa-CpMO- Y75G.G76K, Ala-Cpn10-Y75GK, Ala-Cpn10-D94K, Ala-Cpn10-Y75K,D94K, Ala-Cpn10-D94N, AIa- Cpn10-E34Q, AIa-CpM 0-E34Q,Y75K, Cpn10- ⁇
  • Figure 8 shows a tight correlation between high affintiy binders and reduced NFKB levels compared to AIa-CpMO and X-CpMO.
  • mutants with comprimised affinities for PRR ligands such as AIa-CpM 0-Y75D and Cpn10- ⁇ barrel,Y75K, had an increased level of NFKB activation compared to AIa-CpMO and X-CpMO.
  • CpMO variants were next assessed for their abilities to reduce proinflammatory NFKB activation (from HEK cells expressing TLR3) and IFN- ⁇ production (from human PBMCs) when stimulated with poly(l:C) and CpG-ODN class A, respectively.
  • Example 6 Cpn10 mutants inhibit poly(l:C)-induced NFKB production through TLR-3 in HEK293 cells
  • HEK293 cells were transiently transfected with TLR3 and the pNIFTY-NF ⁇ B luciferase reporter gene. 24 hours post transfection cells were plated out into 24 well plates at 1 x 10 5 and left to adhere overnight. Cells were then stimulated for 18 hours with 0.1 ug poly(l:C) in the presence or absence of 100ug the Cpn10 mutants and 1OuI of SUPERase RNAse inhibitor (Ambion) as a competition assay (Fig. 9). PoIy(LC) and Cpn10 were mixed together at the required concentrations for 30 mins before being added to the cells. Three replicates of each condition were tested. 18 hours post stimulation cells were lysed and luciferase counts were measured. Luciferase counts were normalized to poly(l:C) alone, which was given the value of 100%.
  • Ala-Cpn10 When the cells were stimulated with poly(l:C), Ala-Cpn10 was able to reduce the level of luciferase (ie NFKB) by 22%.
  • Several of the mutants, Ala-Cpn10-Y75K, X-Cpn10-Y75K, Ala-Cpn10-D94K, Ala-Cpn10-Y75G,G76K, AIa-CpM 0-Y75GK and AIa-CpM 0-E34Q,Y75K show significant modulation of Poly(l:C) induced TLR3, with AIa-CpM 0-Y75K reducing signalling by 53%, X-CpMO- Y75K reducing signalling by 71% and AIa-CpM 0-D94K reducing signalling by 82%, for example (fig. 9). This indicates that most of the CpMO mutants have the ability to modulate the immune system, particularly, when involving TLR3 signalling.
  • Example 7 CpMO effect on interferon- ⁇ production from PBMCs in the presence of CpG-A
  • CpMO mutants described herein have an effect on interferon- ⁇ production from PBMCs in the presence of CpG-A
  • human PBMC were isolated from buffy coats, counted and diluted to 3x10 6 cells/ml. 3ml of cells were plated in each well of a 6 well plate, together with 10ug CpMO and 0.25uM CpG-A (ODN2216, InvivoGen). Cells were incubated for 18hrs at 37 0 C, 5% CO2, after which the supematants were removed and assayed for interferon- ⁇ levels using ELISA. As shown in Figure 10, CpMO mutants such as X-Cpn10-Y75K, AIa-CpM 0-Y75K, AIa-
  • mutants such as AIa- Cpn10-Y75K, X-CpM0-Y75K, AIa-CpM 0-Y75G.G76K, AIa-CpM 0-Y75GK, AIa-CpM 0-D94K and AIa-CpM 0-E34Q.Y75K showed significantly increased activity compared to AIa-CpMO and X- CpMO ( Figures 9 and 10).
  • AIa-CpM 0-Y75R also had significantly increased activity in the CpG- ODN class A assay but wild-type activity in the poly(l:C) assay.
  • mutants with comprised (Ala-CpM0-Y75D and CpMO- ⁇ barrel,Y75K) or similar (Ala-Cpn10-Y75H) binding characteristics to Ala-Cpn10 also displayed equivalent activities.
  • the inventors produced a number of Cpn10 polypeptides with various mutations to assess the importance of various amino acid residues (e.g. such as charge and positioning in the Cpn10 molecule) in their ability to have an increased binding to a PRR ligand, such as poly(l:C) and several classes of ODNs compared to such Cpn10 molecules as X-Cpn10 and Ala-Cpn10.
  • various amino acid residues e.g. such as charge and positioning in the Cpn10 molecule
  • a PRR ligand such as poly(l:C)
  • several classes of ODNs compared to such Cpn10 molecules as X-Cpn10 and Ala-Cpn10.
  • the inventors have substituted at least one of amino acid residue at position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41, 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, 96 or any combination thereof of human Cpn10 with a positively charged or neutral residue according to the following table.
  • the inventors have either replaced a neutral amino acid residue with a positively charged residue or replaced a negatively charged amino acid residue with a neutral or positively charged residue.
  • Cpn10 polypeptides with any combination of two or more of the above mutations such as double mutants (e.g. AIa-CpMO- E74K.Y75E, AIa-CpM 0-Y75G.G76K, AIa-CpM O- Y75K.D94K and AIa-CpM 0-E34Q.Y75K).
  • double mutants e.g. AIa-CpMO- E74K.Y75E, AIa-CpM 0-Y75G.G76K, AIa-CpM O- Y75K.D94K and AIa-CpM 0-E34Q.Y75K.
  • additional mutants which include any one or more mutations as listed above with the partial or substantial deletion of one or more loop regions of the CpMO molecule such as the mobile loop and the roof loop.
  • the inventors have constructed the following Cpn10 polypeptide mutants: Cpn10- ⁇ Nterm,Y75K, X-Cpn10- ⁇ ml,Y75K and Cpn10- ⁇ barrel,Y75K. It is contemplated herein that any combination of the above mutations that results in the creation of additional double mutants, triple mutants, and so on, are within the scope of the invention.
  • AIa-CpM 0-Y75K had significantly improved affinity for poly(l:C), CpG-ODN classess-A ⁇ B ⁇ C and E.coli K12 ssRNA compared to AIa-CpMO ( Figures 4 to 7) which could be attributed to not only increasing the net positive charge of the CpMO molecule through amino acid substitutions, deletions, and/or insertions but the location of the mutation and the size of the particular side chains of one or more of the amino acid residues comprising the mutation.
  • the inventors have found that high affinity binding could be achieved by introducing positive charge at several locations under the CpMO dome and that addition of multiple positive charges under the CpMO dome would provide cumulative tigher binding to proinflammatory nucleic acid-based ligands of PRRs.
  • CpMO mutants with high affinity for proinflammatory nucleic acid-based ligands of PRRs can be generated by adding positive or deleting negative residues under the CpMO dome or on flexible structures (ie mobile loops and roof loops) that can move under the dome.
  • the examples as laid out above show that several Cpn10 mutants as described herein have higher affinities for nucleic acid-based PRR ligands which is indicative of increased immunomodulatory activity in cell based assays of inflammation.

Abstract

The present invention relates to an isolated Cpn10 polypeptide possessing an increased affinity for a PRR ligand compared to a wild-type Cpn10 polypeptide. In a further embodiment, the present invention also relates to modified chaperonin 10 polypeptides, and to nucleic acids encoding the same and to compositions comprising such polypeptides and uses thereof.

Description

MODIFIED CHAPERONIN 10 AND PRR SIGNALING
Field of the Invention
The present invention relates to modified chaperonin 10 polypeptides, and to nucleic acids encoding the same. The present invention further relates to mutants of chaperonin 10 and to compositions comprising such polypeptides.
Background
Mammalian chaperonin 10 (Cpn10), also known as heat shock protein 10 (Hsp10) and early pregnancy factor (EPF), is typically characterised as a mitochondrial 'molecular chaperone' protein involved in protein folding together with chaperonin 60 (Cpn60), also known as heat shock protein 60 (Hsp60). Cpn10 and Cpn60 are homologues of the bacterial proteins GroES and GroEL respectively. GroES and Cpn10 each oligomerise into seven member rings that bind as a lid onto a barrel-like structure comprising fourteen GroEL or seven Cpn60 molecules respectively, which tether denatured proteins to the complex (Bukau and Horwich, 1998, Cell 92:351-366; Hartl and Hayer-Hartl, 2002, Science 295:1852-1858). Cpn10 proteins are highly conserved across species. Human Cpn10 is 100% identical to bovine, canine, ovine and porcine Cpn10 and differs from rat Cpn10 at only a single amino acid position. Human Cpn10 shares 30% sequence identity (60% similarity) with GroES from Escherichia coll Cpn10/GroES proteins are dome shaped heptameric rings wherein each monomer is comprised of essentially three different structural regions, a core anti-parallel β-barrel region flanked by a "roof β-hairpin loop region and a "mobile loop" region. The anti-parallel β- barrel region of each monomer forms the core of a dome and when assembled in the heptamer the β-hairpin loops of each monomer form the roof of the dome. In each monomer, the mobile loop region is at the opposite end of the β-barrel to the roof loops. A section of the anti-parallel β-barrel region forms an inward facing lower rim region of the cavity. This lower rim region contains a number of phylogenetically conserved amino acids including a Tyrosine at position 75 (Y75).
In addition to its intracellular role as a molecular chaperone, Cpn10 is also frequently found at the cell surface (see Belles etai, 1999, Infect lmmun 67:4191-4200) and in the extracellular fluid (see Shin et al., 2003, J Biol Chem 278:7607-7616) and is increasingly being recognised as a regulator of the immune response. However the sites within the Cpn10 molecule responsible for mediating this immunomodulatory activity have remained elusive. The present invention relates to the discovery that modification of Cpn10 affects the immunomodulatory activity of Cpn10, in particular its role in binding ligands of pattern recognition receptors (PRRs) such as Toll-like Receptors (TLR), Nucleotide-binding domain LRR-containing family (NLR), RIG-l-like receptors (RLR), DNA- dependent activators of IRF (DAI) and C-type Lectin receptors (CLR).
Summary
According to a first aspect of the present invention there is provided an isolated Cpn10 polypeptide possessing an increased affinity for a PRR ligand compared to a wild-type Cpn10 polypeptide.
The PRR may be a Toll-like Receptor (TLR), Nucleotide-binding domain LRR-containing family (NLR), RIG-l-like receptor (RLR), DNA-dependent activator of IRF (DAI) or C-type Lectin receptor (CLR).
The TLR may be selected from the group comprising of at least one of TLR3, TLR7, TLR8 or TLR9. For example, the TLR is TLR3.
The ligand may be an agonist or antagonist. In one embodiment, said polypeptide possesses a greater net positive charge compared to the wild-type Cpn10 polypeptide. In another embodiment, one or more wild-type Cpn10 polypeptides may form a wild-type CpniO molecule. For example, the CpIO molecule may be a heptamer molecule comprising Cpn10 polypeptide subunits.
In another embodiment, the isolated polypeptide possesses at least one mutation under the dome of the wild-type Cpn10 molecule. The mutation may be an amino acid substitution, addition or deletion. The substitution may be the replacement of one or more amino acid residues with one or more positively charged or neutral residues or a combination thereof. In another embodiment, a negatively charged residue may be replaced with a neutral or positively charged residue.
In another embodiment, a neutral residue may be replaced with a positively charged residue. The positively charged residue may be arginine (R), lysine (K) or histidine (H). The neutral residue may be asparagine (N), glutamine (Q), serine (S), threonine (T), glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), tyrosine (Y), tryptophan (W), cysteine (C), methionine (M) or H (above pH 6.04).
In another embodiment, the mutation under the dome may be a mutation in either the mobile loop, or the roof loop, or at a position wherein the residue has free side chains within the inner surface of the Cpn10 molecule, or a combination thereof.
In yet another embodiment, the polypeptide comprises a mutation at an amino acid position selected from the group consisting of position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41, 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, and 96 of the wild-type Cpn10 molecule or a combination thereof.
In a further embodiment, said polypeptide comprises a mutation selected from the group consisting of F12K, D13K, A21K, A22K, E23K, T24K, V25K, T26K, G28K, G29K, I30K, M31K, L32K, P33K, E34K, S36K, Q37K, G38K, V40K, L41K, S52K, G54K, G56K, G57K, E58K, I59K, Q60K, P61K, V62K, E74K, Y75K, G76K, G77K, T78K, V81K, D84K, D86K, F88K, L89K, D92K, G93K, D94K, L96K, F12R, D13R, A21R, A22R, E23R, T24R, V25R, T26R, G28R, G29R, I30R, M31R, L32R, P33R, E34R, S36R, Q37R, G38R, V40R, L41R, S52R, G54R, G56R, G57R, E58R, I59R, Q60R, P61R, V62R, E74R, Y75R, G76R, G77R, T78R, V81R, D84R, D86R, F88R, L89R, D92R, G93R, D94R, L96R, F12H, D13H, A21H, A22H, E23H, T24H, V25H, T26H, G28H, G29H, I30H, M31H, L32H, P33H, E34H, S36H, Q37H, G38H, V40H, L41H, S52H, G54H, G56H, G57H, E58H, I59H, Q60H, P61H, V62H, E74H, Y75H, G76H, G77H, T78H, V81H, D84H, D86H, F88H, L89H, D92H, G93H, D94H, L96H, D13N, E23Q, E34Q, E58Q, E74Q, D84N, D86N, D92N, D13G, E23G, E34G, E58G, E74G, D84G, D86G, D92G, D13A, E23A, E34A, E58A, E74A, D84A, D86A, D92A, D13V, E23V, E34V, E58V, E74V, D84V, D86V, D92V, D13L, E23L, E34L, E58L, E74L, D84L, D86L, D92L, D13I, E23I, E34I, E58I, E74I, D84I, D86I, D92I, D13P, E23P, E34P, E58P, E74P, D84P, D86P, D92P, D13F, E23F, E34F, E58F, E74F, D84F, D86F, D92F, D13Y, E23Y, E34Y, E58Y, E74Y, D84Y, D86Y, D92Y, D13W, E23W, E34W, E58W, E74W, D84W, D86W, D92W, D13C, E23C, E34C, E58C, E74C, D84C, D86C, D92C, D13M, E23M, E34M, E58M, E74M, D84M, D86M, D92M, D13S, E23S, E34S, E58S, E74S, D84S, D86S, D92S, D13T, E23T, E34T, E58T, E74T, D84T, D86T, D92T, D13H, E23H, E34H, E58H, E74H, D84H, D86H, D92H or a combination thereof.
In a further embodiment, the polypeptide may comprise two or more mutations. For example, the polypeptide may comprise mutations selected from the group comprising E74K,Y75E; Y75G,G76K; Y75K,D94K and E34Q,Y75K.
In another embodiment, the polypeptide may lack, or substantially lack, the N-terminus, the mobile loop, the β-hairpin roof loop or a combination thereof. For example, the polypeptide may be selected from the group consisting of Cpn10-ΔNterm-Y75K, X-Cpn10-Δml-Y75K and Cpn10-β- barrel-Y75K. The polypeptide may comprise an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58 and 61-102.
The polypeptide may comprise mutations selected from the group consisting of Y75K, Y75R, (Y75G,G76K), Y75GK, D94K, D94N, (Y75K,D94K) and (E34Q,Y75K). The polypeptide may comprise an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 31, 37, 43, 49, 52 and 55.The polypeptide may be naturally-derived, recombinantly produced or synthetically produced. The Cpn10 may be of eukaryotic origin. The polypeptide may be of mammalian origin. The polypeptide may be human Cpn10.
According to a second aspect of the present invention there is provided an isolated nucleic acid encoding a polypeptide according to the first aspect. In one embodiment, the isolated nucleic acid may comprise a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 17-18, 20-21, 23-24, 26-27, 29-30, 32-33, 35-36, 38-39, 41-42, 44-45, 47-48, 50-51, 53-54, 56-57 and 59-60. In a further embodiment, the isolated nucleic acid may comprise a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 32-33, 35-36, 50-51, 53-54 and 56-57. According to a third aspect of the present invention there is provided an expression construct comprising a nucleic acid according to the second aspect operably-linked to one or more regulatory sequences.
The nucleic acid may be a codon optimised Cpn10 nucleic acid. The codon optimised nucleic acid sequence may have one or more nucleotide substitutions that increase the utilisation of transfer RNA pools, exploit more efficient stop codons, remove RNA secondary structures and/or destabilising elements.
According to a fourth aspect of the present invention there is provided a host cell expressing a polypeptide of the first aspect, or comprising a nucleic acid of the second aspect or an expression construct of the third aspect. According to a fifth aspect of the present invention there is provided an antibody that selectively binds to a polypeptide of the first aspect.
According to a sixth aspect of the present invention there is provided a pharmaceutical composition comprising a polypeptide of the first aspect, a nucleic acid of the second aspect or an expression construct of the third aspect or an antibody of the fifth aspect. According to a seventh aspect of the present invention there is provided a method of treating a subject, including the step of administering to said subject a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
The treatment may modulate the immune response in the subject. The immune response may be modulated via regulation of PRR signalling. According to an eighth aspect of the present invention there is provided a method for treating or preventing a disease, disorder or condition in a subject, the method comprising administering to the subject an effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
The disease, disorder or condition may be selected from acute or chronic inflammatory diseases such as, insulin dependent diabetes mellitus, systemic lupus erythematosis, Sjorgren's disease, Graves disease, multiple sclerosis, rheumatoid arthritis, chronic fatigue syndrome, Alzheimer's disease, asthma, allergy, multiple sclerosis, GVHD, artherosclerosis, inflammatory pain or an infectious disease. The infectious disease may result from a bacterial, viral, or fungal infection. According to a ninth aspect of the present invention there is provided a method for modulating PRR signalling in a subject, or in at least one cell, tissue or organ thereof, the method comprising administering a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
According to a tenth aspect of the present invention there is provided a method for modulating the production and/or secretion of one or more immunomodulators in a subject, or at least one cell, tissue or organ thereof, the method comprising administering a therapeutically effective amount of a Cpn10 polypeptide of the first aspect or a nucleic acid of the second aspect.
The polypeptide may modulate signalling from a PRR by binding a PRR ligand. The immunomodulator may be a pro-inflammatory cytokine or chemokine or an anti-inflammatory cytokine or chemokine. The cytokine or chemokine may be selected from TNF-α, IL-1 , IL-6, RANTES, IL-10, TGF-β or a type I interferon. The type I interferon may be IFNα or IFNβ.
According to an eleventh aspect of the present invention there is provided a method for inhibiting the production and/or secretion of one or more immunomodulators in a subject, or at least one cell, tissue or organ thereof, the method comprising administering an effective amount of a Cpn 10 polypeptide of the first aspect or a nucleic acid of the second aspect.
The polypeptide may modulate signalling from a PRR by binding a PRR ligand. The immunomodulator may be a pro-inflammatory cytokine or chemokine or an antiinflammatory cytokine or chemokine. The cytokine or chemokine may be selected from TNF-α, IL-1 , IL-6, RANTES, IL-10, TGF-β or a type I interferon. The type I interferon may be IFNα or IFNβ. According to a twelfth aspect of the present invention there is provided a method of identifying a compound that binds to a polypeptide of the first aspect, the method comprising the steps of:
(a) contacting a candidate compound with said polypeptide; and
(b) assaying for the formation of a complex between the candidate compound and said polypeptide.
The assay for the formation of a complex may be a competitive binding assay, a two-hybrid assay, an electrophoretic mobility shift (gel-shift) assay and/or a plate capture assay. The assay may be qualitative or quantitative. According to a thirteenth aspect of the present invention there is provided a method of screening for a compound that modulates the activity of a polypeptide of the first aspect, the method comprising the steps of:
(a) contacting said polypeptide with a candidate compound under conditions suitable to enable interaction of said candidate compound to said polypeptide; and
(b) assaying for activity of said polypeptide.
Assaying for activity of the polypeptide may comprise a step of adding a labelled substrate and measuring a change in the labelled substrate.
According to a fourteenth aspect of the present invention there is provided a method of screening for a PRR ligand, the method comprising the steps of:
(a) contacting a polypeptide of the first aspect with a candidate PRR ligand compound under conditions suitable to enable interaction of said candidate compound to said polypeptide; and
(b) assaying for increased affinity of said compound with said polypeptide compared to wild type Cpn 10; and/or (c) assaying for decreased or increased PRR activation in the presence of the candidate
PRR ligand compound and the polypeptide of the first aspect.
The invention also contemplates variants, derivatives, homologues, analogues and fragments of the isolated Cpn10 polypeptides and polynucleotides according to the above aspects and embodiments. According to the above aspects and embodiments, the Cpn 10 polypeptides and polynucleotides may be derived from any animal, may be generated using recombinant DNA technologies or may be synthetically produced. Cpn10 may be a eukaryotic Cpn10. For example, Cpn10 is human Cpn10.
The wild-type Cpn10 molecule or polypeptide may be acetyl-Cpn10 (SEQ ID No. 1) or X- Cpn10 (SEQ ID No. 6).
According to the above aspects and embodiments the immunomodulatory activity of a Cpn 10 polypeptide may involve generation of heptamers of the polypeptide.
Definitions
In the context of this specification, the term "comprising" means "including principally, but not necessarily solely". Furthermore, variations of the word "comprising", such as "comprise" and "comprises", have correspondingly varied meanings.
The term "wild-type" as used herein in relation to Cpn 10 molecules or polypeptides includes native or non-native forms. For example, native human Cpn 10 is acetylated at its N-terminus. The present invention contemplates, within the scope of the term wild-type, acetylated or non-acetylated Cpn10 molecules. The wild-type Cpn10 molecule may be acetyl-Cpn10 or X-Cpn10 as represented by SEQ ID Nos. 1 or 6 respectively.
The term "immunomodulator" means a molecular mediator which interacts with the immune system and that plays a role in the activation, inhibition, modulation, maintenance, maturation, suppression or augmentation of an immune response.
The term "Pattern recognition receptors" or PRRs as used herein means several classes of germline-encoded proteins including Toll-like receptors (TLRs), Nucleotide-binding domain LRR-containing family (NLRs), RIG-l-like receptors (RLRs), DNA-dependent activators of IRF (DAIs) or C-type Lectin receptosr (CLRs) (see for example Akira et al., Cell 2006, 124: 783- 801 ; Latz, E. and Fitzgerald, K. A. (2008) Nat. Rev. Immunol. Vol. 8, No. 4, Poster).
The term 'Toll-like receptors" or TLRs means receptors which interact with pathogens and initiate the host immune response to infection. In mammals, activation of TLRs by pathogens sets in motion an innate immune inflammatory process that prevents pathogen dissemination and, through TLRs on dendritic cells, directs the development of acquired immunity. The TLRs are encoded by a limited number of genes in the germline, 10 known in humans. These 10 receptors recognize a wide variety of pathogen-derived molecular signatures, including glycolipids such as lipopolysaccharide, proteins such as flagellin, and nucleic acids such as dsRNA. TLRs can be divided into two groups, cell surface TLRs which generally recognize hydrophobic ligands and intracellular TLRs (i.e. TLR-3, TLR-7, TLR-8 and TLR-9) which generally recognize nucleic acid based ligands.
As used herein the terms "modulating", "modulates" and variations thereof refer to increasing or decreasing the level of activity, production, secretion or functioning of a molecule in the presence of a particular modulatory molecule or agent of the invention compared to the level of activity, production, secretion or other functioning thereof in the absence of the modulatory molecule or agent. These terms do not imply quantification of the increase or decrease. The modulation may be of any magnitude sufficient to produce the desired result and may be direct or indirect.
The term "net charge" as used herein refers to the charge of a molecule. Molecules that comprise an amino acid sequence such as proteins, peptides, and polypeptides (e.g. Cpn10 polypeptide) can either be positively or negatively charged. The net charge of a molecule can be calculated by subtracting the number of the acidic amino acid residues from that of the basic ones. In addition, net charge may be determined by its correlation to isoelectric focusing (e.g. pi as shown in Example 2) which takes place in a pH gradient and is produced by an electric field. Before an electric field is applied the gel has a uniform pH-value and almost all the carrier molecules are charged. When an electric field is applied, the negatively charged molecules move towards the anode, the positively charged ones to the cathode. The molecules align themselves in between the cathode and the anode at a pH environment where they have a net neutral charge (i.e. at their pl- value).
The term "net positive charge" as used herein is the overall charge of a molecule wherein the number of basic amino acid residues are greater than the number of acidic ones in the molecule and/or the molecule's migration to the cathode when applied to electric field within a molecular technique such as isoelectric focusing.
The term "under the dome" as used herein means the inner surface of the dome of the
Cpn10 molecule which is located inside the heptameric ring of identical 10 kDa Cpn10 subunits (Figure 1). The regions of Cpn10 molecule that are under the dome include the mobile loop and the roof loop which protrude from an irregular β-barrel topology of each Cpn10 subunit, the lower rim region and any residue that has free side chains within the inner surface of the molecule such as
F12, D13, R14, R19, V40, L41, G77, T78, K79, V81, D84, D86, F88, L89, R91, D92, G93, D94 and
L96 (residue numbering is based on either X-Cpn10 (SEQ ID No. 6) or acetyl-Cpn10 (SEQ ID No. 1 ) as described herein).
The term "mobile loop" is a flexible region of the Cpn10 molecule that comprises 18 amino acid residues. The mobile loop comprises residues A21 to G38 (see Figure 1; residue numbering is based on either X-Cpn10 (SEQ ID No.6) or acetyl-Cpn10 (SEQ ID No. 1) as described herein).
The term "roof loop" is a flexible region of the Cpn10 molecule that comprises 14 amino acid residues. The roof loop comprises residues S52 to V62 (see Figure 1 ; residue numbering is based on either X-Cpn10 (SEQ ID No. 6) oracetyl-Cpn10 (SEQ ID No. 1) as described herein).
The term "lower rim region" as used herein means the collection of amino acids surrounding Tyrosine (Y) 75 of human Cpn10 (or its equivalent in other homologues). For example, the lower rim region comprises at least the amino acid residues Glutamic Acid (E) 74,Tyrosine (Y) 75, and Glycine (G) 76 of human Cpn10 (or its equivalent in other homologues).
The term "amino acid" as used herein means any molecule that contains both amine and carboxyl functional groups.
The term "charged residue" as used herein means any amino acid residue with a side-chain that has the potential to carry a positive or negative charge. The term "polypeptide" means a polymer made up of amino acids linked together by peptide bonds. The term "polypeptide" may constitute a portion of a full length protein. Further, the term "polypeptide" refers to a polypeptide that may exhibit at least one modification of its amino acid sequence, compared to a wild type Cpn10 molecule. The modification may include chemical modifications such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which are naturally occurring in human proteins.
The term "polynucleotide" as used herein refers to a single- or double- stranded polymer of deoxyribonucleotide, ribonucleotide bases or known analogues of natural nucleotides, or mixtures thereof. The term includes reference to the specified sequence as well as to the sequence complimentary thereto, unless otherwise indicated. The terms "polynucleotide" and "nucleic acid" are used interchangeably herein.
The term "isolated" means that the molecule in question has been removed from its natural environment or host, and associated impurities reduced or eliminated such that the molecule in question is the predominant species present (e.g., on a molar basis it is more abundant than any other individual species in the composition/sample). Typically a substantially purified fraction is a composition wherein the object species comprises at least about 30 percent of all macromolecular species present. Generally, a substantially pure composition will comprise more than about 80 to 90 percent of all macromolecular species present in the composition. Most typically, the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
As used herein the term "substantially" means the majority but not necessarily all, and thus in relation to a modified polypeptide "substantially" lacking a component region of a corresponding wild-type polypeptide, the modified polypeptide may retain a portion of that component region. For example, a modified polypeptide "substantially" lacking a component region of a corresponding wild-type polypeptide may retain approximately 50 percent or less of the sequence of the component region, although typically the component region is rendered structurally and/or functionally inactive by virtue of the proportion of the sequences of the region omitted.
The term "conservative amino acid substitution" as used herein refers to the replacement of one amino acid with another amino acid having similar structural and/or chemical properties. Conservative amino acid substitutions may be made on the basis of similarity in one or more of the following: polarity, charge, solubility, hydrophobic^, hydrophilicity, and/or the amphipathic nature of the residues involved. For example, nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tyrosine, tryptophan, cysteine and methionine; polar uncharged amino acids include glycine, serine, threonine, asparagine, and glutamine; polar positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Amino acid "Insertions" or "deletions" are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids. The variation may be experimentally determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity. As used herein the terms "treatment", "treating" and variations thereof, refer to any and all uses which remedy a disease state or symptoms, prevent the establishment of disease, or otherwise prevent, hinder, retard, or reverse the progression of disease or other undesirable symptoms in any way whatsoever.
As used herein the term "effective amount" includes within its meaning a non-toxic but sufficient amount of an agent or compound to provide the desired therapeutic or prophylactic effect. The exact amount required will vary from subject to subject depending on factors such as the species being treated, the age and general condition of the subject, the severity of the condition being treated, the particular agent being administered and the mode of administration and so forth. Thus, it is not possible to specify an exact "effective amount". However, for any given case, an appropriate "effective amount" may be determined by one of ordinary skill in the art using only routine experimentation.
Brief Description of the Drawings
Figure 1. A. Crystal structure of E. coli Cpn10 (GroES) showing the anti-parallel β-barrel, the roof β-hairpin loop and mobile loop regions. Cpn10 is comprised of seven identical 1OkDa subunits. The mobile loop residue G29, phylogenetically conserved aromatic residue Y71 and negatively charged residue D91 are shown. B. Amino acid sequence of E. coli GroES (SwissProt P0A6F9) and wild-type human Cpn10 (SwissProt P61604 and GenBank X75821). The 18 amino acid mobile loop and 14 amino acid roof β-hairpin are shown. GroES residues G29 (Cpn10 E34), Y71 (Cpn10 Y75) and D90 (Cpn10 D94) are shaded grey. The GroES residue G29 (E34 in human Cpn10) resides in the mobile loop. The phylogenetically conserved aromatic residue (Y75 in human Cpn10 and Y71 in GroES) resides under the dome on the lower rim region (comprised of the loop residues E74, Y75 and G76 in human Cpn10). The negatively charge D94 residue (D90 in GroES) residues under the dome on a loop above the Y75 containing lower rim region. The GroES ribbon structure was created from the X-ray crystal coordinates published by Xu et al. (Nature 1997, 388: 741-750), in this structure the usually disordered mobile loops are perfectly aligned through interaction with GroEL (GroEL was omitted in the diagram).
Figure 2. Sequence alignment of human Cpn10 with Cpn10 homologs from numerous biological kingdoms. Amino acids that are different to human Cpn10 are shaded yellow. The location of the mobile loop (blue), β-hairpin roof loop (red) and conserved tyrosine reside in the lower rim region (green; amino acid 75 in human Cpn10 and 71 in E.coli GroES) is indicated. Boxes (marked a to e) indicate the predicted boundaries of the 55 residue β-barrel core (Hunt et ai, 1997 Cell 90: 361-371). The percentage identity and similarity of the various homologs relative to human Cpn10 is shown. The SwissProt accession number of each protein is given. Calculation of sequence % identity and % similarity to human Cpn10 was performed with NCBI blast (Altschul et ai, 1997 Nucleic Acids Res. 25:3389-3402), NS = no significant similarity found. Isoelectric points (pi) were calculated using the ExPASy proteomics server ProtParam Tool (www.expasy.org/tools/protparam.html). Figure 3. SDS-PAGE stained with Coomassie brilliant blue reveals that recombinant Cpn10 proteins are >99% pure.
Figure 4. 1μg of TLR3 agonist PoIy(IrC) (a synthetic dsRNA analog) was incubated with 50μg of a Cpn10 variant and the indicated salt concentration in 1OmM Tris-HCI (pH7.6) for 1hr at 230C. Samples were resolved in a 1% TAE agarose gel and stained successively with Ethidium Bromide and Coomassie brilliant blue. Free Cpn10 migrates towards the negative electrode (top of the gel) while free poly(l:C) migrates towards the positive electrode (bottom of the gel), complexes of Cpn10-poly(l:C) retard the movement of both molecules.
Figure 5. 1μg of human ODN-2216 class A, human ODN-2006 class B or ODN-M362 class C (TLR9 agonists; Invivogen) were incubated with 50μg of Cpn10 in 1OmM Tris-HCI (pH7.6) and the indicated salt concentration for 15min at 230C. Samples were resolved in a 1% TAE agarose gel and stained with ethidium bromide. Free CpMO migrates towards the negative electrode (top of the gel) while free CpG-ODNs migrate towards the positive electrode (bottom of the gel), complexes of Cpn10-CpG-ODNs retard the movement of both molecules.
Figure 6. 0.5μg of E.coli K12 ssRNA (Invivogen Cat# tlrl-ecrna) (TLR7/8 agonist) was incubated with 50μg of a Cpn10 variant, in 1OmM Tris-HCI (pH 7.6) and the indicated salt concentrations (0, 150 and 50OmM NaCI) for 30mins at 370C. Samples were resolved in a 1% TAE agarose gel and stained with Ethidium Bromide. Free Cpn10 migrates towards the negative electrode (top of the gel) while free ssRNA migrate towards the positive electrode (bottom of the gel), complexes of Cpn10-CpG-ODNs retard the movement of both molecules. Figure 7. Quantitative analysis of Cpn10 binding to CpG oligonucleotides (ODNs). AIa-
Cpn10 and Cpn10 mutants were formulated at Iμg/μl in formulation buffer pH7.2 (Invitrogen) and 50μg was adsorbed to triplicate wells of a 96 well plate 16 hr at 40C. Following the decanting of non-bound protein, the plate was blocked with 1% BSA and 5% sucrose in PBS pH7.2 for 2hr at 230C. 50μl of 3'-biotin labeled human ODN-2216 class-A, human ODN-2006 class-B, or human ODN-M362 class-C (TLR9 agonists) (Proligo/Sigma) formulated at 0.02 μg/μl in PBS pH 7.2 was added to each well and incubated for 2hr at 230C. Unbound ligand was removed with five PBS (pH7.2) + 0.05% Tween 20 washes. Bound CpG-ODNs were analysed with a Streptavidin-HRP and TMB detection system at A450nm. The results are the average of three replicates and are normalized to the level of binding of Ala-Cpn10 to each CpG. Figure 8. Cpn10 modulates CpG-B ODN-induced NFKB activity. RAW264.7 (mouse macrophage) cells were transfected with pNifty NFκB-luciferase reporter plasmid (InvivoGen) using Genejuice according to the manufacturers instructions (Novogen). 24 hours later cells were trypsinised, counted and 2.5 x 105 cells were plated in 1ml of media into each well of a 24 well plate and left to adhere overnight. 100μg of a Cpn10 construct or Formulation buffer control was mixed with 4 μg of CpG-B ODN-1826 (Invivogen) and passed through a centrifugal filter device YM10 (Amicon). The entire flow through volume was added to the RAW264-pNIFty-LUC cells and incubated at 370C for 5 hours. Cells were washed and subsequently lysed with 100 μ I per well of CCLR 1 X solution (Promega luciferase lysis buffer), mixed with luciferase substrate following the manufactures instructions and the luciferase counts measured. Figure show NFKB activation levels normalized to Ala-cpn10 at 100%.
Figure 9. Effect of Cpn10 mutants on Poly (I:C) stimulation. HEK293 cells were transiently transfected with plasmids encoding for TLR3 and pNifty NFkB-luciferase (InvivoGen) using GeneJuice according to the manufacturers instructions (Novogen). 24hours later the transfected cells were trypsinised, counted and 1x105 cells were plated in 1ml of media into each well of a 24 well plate and allowed to adhere for 24hrs. Then 100ug of Cpn10, 0.1 ug Poly (I:C) (InvivoGen) and 1OuI of SUPERase RNAse inhibitor (Ambion) were added to each well for 24hrs. The supematants were then removed, the cells wash in PBS and lysed with 1x Lysis Buffer (Promega), and assayed for luciferase. Levels of luciferase were normalized to Poly (I:C) alone at 100%. Values represent the mean of triplicate wells. Figure 10. Cpn10 effect on interferon-α production from PBMCs in the presence of CpG-A.
Human PBMC were isolated from buffy coats, counted and diluted to 3x106 cells/ml. 3ml of cells were plated in each well of a 6 well plate, together with 10ug Cpn10 and 0.25uM CpG-A (ODN2216, InvivoGen). Cells were incubated for 18hrs at 370C1 5% CO2, after which the supematants were removed and assayed for interferon-α levels using ELISA. Results were normalized to Ala-Cpn10 at 100%. Figure represents the mean of 3-5 replicate experiments.
Detailed Description
Cpn10 is a dome-shaped, heptameric ring of identical 10 kDa subunits (Figure 1). The surface of the dome is hydrophilic and highly charged. Each Cpn10 subunit forms an irregular β- barrel topology from which two large extensions protrude. The first extension is a β-hairpin loop that extends towards the centre of the heptamer and forms the roof of the dome-like structure. Intriguingly, whereas the roof of GroES (E. coli Cpn10) contains a cluster of negatively charged residues at the tips of the roof loops under physiological conditions, the roof of mammalian Cpn10 contains a positively charged cluster of amino acids at the tips of the roof loops; while a large portion of the roof is missing completely from the bacteriophage Cpn10 (Gp31). The molecule also has another extension that is a flexible 18 amino acid mobile loop that extends from the base of the dome and mediates an interaction with Cpn60. A smaller loop, comprised of residues Glu-74, Tyr- 75 and Gly-76, extends from the base of the dome and protrudes inwards to form a lower rim region. The amino acid residues in the lower rim region are phylogenetically conserved amongst most eukaryotes.
Without being bound to any mechanism or pathway, the inventors have generated a series of mutations through primarily amino acid substitutions which modify the net charge of a wild-type Cpn10 polypeptide and demonstrated herein that these mutations which are located under the dome are effective jn modifying the interaction of Cpn10 with one or more PRR ligands, specifically increasing the binding affinity of Cpn10 with the PRR ligand, which indicates an ability to immunomodulate the immune system/response through PRR signalling.
Pattern Recognition Receptors (PRRs), including Toll-like receptors (TLRs), Nucleotide- binding domain LRR-containing family (NLR), RIG-l-like receptor (RLR), DNA-dependent activator of IRF (DAI) and C-type Lectin receptor (CLR), are the sentinels of the immune system, they act as the first line of defense against invading pathogens, recognising specific pathogenic associated molecular patterns (PAMPS) and initiating an immune response. It appears that PRRs also play a role in many inflammatory syndromes, including sepsis, autoimmune or chronic inflammatory diseases where altered self molecules hyperactivate PRRs leading to the development of a pathological state.
CpnW polypeptide mutants
As described herein, the present invention provides isolated Cpn10 polypeptides possessing an increased affinity for a PRR ligand compared to a wild-type Cpn10 polypeptide such as acetyl- Cpn10 (SEQ ID No.1) and X-Cpn10 (SEQ ID No.6). Further, the present invention provides isolated Cpn10 polypeptides possessing a greater net positive charge compared to the wild-type Cpn10 molecule based on at least one mutation under the dome of the Cpn10. The type of mutation can be, but not limited to, amino acid substitution, addition or deletion in which substitution may be the replacement of a negatively charged residue with a neutral or positively charged residue or where a neutral residue is replaced with a positively charged residue. These mutations which occur under the dome are located within any one of the mobile loop, roof loop, lower rim region and at any amino acid residue position wherein the residue at the position has free side chains within the inner surface of the Cpn10 molecule, or a combination thereof. The positively charged residue may be, but not limited to, arginine (R), lysine (K) or 5 histidine (H). The neutral residue may be, but not limited to, asparagine (N), glutamine (Q), serine (S), threonine (T), glycine (G), alanine (A), valine (V), leucine (L)1 isoleucine (I), proline (P), phenylalanine (F), tyrosine (Y), tryptophan (W), cysteine (C), methionine (M) and H (above pH 6.04). These mutations may occur at residue position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41 , 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, 96 or any combination thereof.o Specifically, the mutation may be selected from the group comprising F12K, D13K, A21K, A22K, E23K, T24K, V25K, T26K, G28K, G29K, I30K, M31K, L32K, P33K, E34K, S36K, Q37K, G38K, V40K, L41K, S52K, G54K, G56K, G57K, E58K, I59K, Q60K, P61K, V62K, E74K, Y75K, G76K, G77K, T78K, V81K, D84K, D86K, F88K, L89K, D92K, G93K, D94K, L96K, F12R, D13R, A21R, A22R, E23R, T24R, V25R, T26R, G28R, G29R, I30R, M31R, L32R, P33R, E34R, S36R, Q37R,s G38R, V40R, L41R, S52R, G54R, G56R, G57R, E58R, I59R, Q60R, P61R, V62R, E74R, Y75R, G76R, G77R, T78R, V81R, D84R, D86R, F88R, L89R, D92R, G93R, D94R, L96R, F12H, D13H, A21H, A22H, E23H, T24H, V25H, T26H, G28H, G29H, I30H, M31H, L32H, P33H, E34H, S36H, Q37H, G38H, V40H, L41H, S52H, G54H, G56H, G57H, E58H, I59H, Q60H, P61H, V62H, E74H, Y75H, G76H, G77H, T78H, V81H, D84H, D86H, F88H, L89H, D92H, G93H, D94H, L96H, D13N,0 E23Q, E34Q, E58Q, E74Q, D84N, D86N, D92N, D13G, E23G, E34G, E58G, E74G, D84G, D86G, D92G, D13A, E23A, E34A, E58A, E74A, D84A, D86A, D92A, D13V, E23V, E34V, E58V, E74V, D84V, D86V, D92V, D13L, E23L, E34L, E58L, E74L, D84L, D86L, D92L, D13I, E23I, E34I, E58I, E74I, D84I, D86I, D92I, D13P, E23P, E34P, E58P, E74P, D84P, D86P, D92P, D13F, E23F, E34F, E58F, E74F, D84F, D86F, D92F, D13Y, E23Y, E34Y, E58Y, E74Y, D84Y, D86Y, D92Y, D13W,s E23W, E34W, E58W, E74W, D84W, D86W, D92W, D13C, E23C, E34C, E58C, E74C, D84C, D86C, D92C, D13M, E23M, E34M, E58M, E74M, D84M, D86M, D92M, D13S, E23S, E34S, E58S, E74S, D84S, D86S, D92S, D13T, E23T, E34T, E58T, E74T, D84T, D86T, D92T, D13H, E23H, E34H, E58H, E74H, D84H, D86H, D92H or a combination thereof. Further, the polypeptide may comprise two or more mutations. For example, the polypeptide may comprise mutations selected0 from the group comprising E74K.Y75E; Y75G.G76K; Y75K.D94K and E34Q.Y75K. The polypeptide may lack, or substantially lack, the N-terminus, the mobile loop, the hairpin roof loop or a combination thereof. For example, the polypeptide may be selected from the group comprising Cpn10-ΔNterm-Y75K, X-Cpn10-Δml-Y75K and Cpn10-βbarrel-Y75K.
The polypeptide may comprise an amino acid sequence selected from the group comprising5 SEQ ID Nos. 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58 and 61-102. Furthermore, the polypeptide may comprise mutations selected from the group comprising Y75K, Y75R, (Y75G.G76K), Y75GK, D94K, D94N, (Y75K.D94K) and (E34Q.Y75K) and comprise an amino acid sequence selected from the group comprising SEQ ID Nos. 10, 13, 31, 37, 43, 49, 52 and 55. It is demonstrated herein that the isolated Cpn10 polypeptides as described herein possess an increased affinity for PRR ligands, in particular the TLR-3 agonist poly(l:C), TLR7 and TLR8 agonist E.coli ssRNA and TLR9 agonists unmethylated CpG-oligonucleotides (ODNs) (ODN-2216 class A, ODN-2006 class B and ODN-M362 class C). It is also demonstrated herein that these Cpn10 polypeptides inhibit poly(l:C) induced NFkB activation and have an effect on interferon production in PBMCs in the presence of CpG oligonucleotides.
Polypeptides
As disclosed herein the present invention contemplates isolated Cpn10 polypeptides, herein, and its increased affinity for a PRR ligand, comprising one or more amino acid deletions, additions or substitutions in comparison with a corresponding wild-type Cpn10 polypeptide such as X-Cpn10 or acetyl-Cpn10.
Cpn10 may be native, naturally-derived, recombinant or synthetic Cpn10. The Cpn10 molecule may be any Cpn10 polypeptide from a eukaryotic organism. By way of example as shown in Figure 2, the Cpn10 may be derived from yeast (e.g. Saccharomyces cerevisiae), nematode (e.g. Caenorhabditis elegans), frog (e.g. Xenopus tropicalis), chicken (e.g. Gallus gallυs), zebrafish (e.g. Danio rerio), fly (e.g. fruit fly such as Drosphila melanogasteή, plant (e.g. Arabidopsis thaliana) or a mammal. The mammalian Cpn10 may be primate, murine, ovine, bovine, canine, feline, porcine or equine. Alternatively the Cpn10 may be archaeal in origin. In particular embodiments the Cpn10 is human Cpn10.
The present invention relates to modifications of Cpn10 polypeptides as disclosed herein and encompasses otherwise wild-type molecules modified by the addition, deletion, or substitution of one or more amino acid residues herein, and how these modifications can increase the affinity of these Cpn10 polypeptides to a PRR ligand. Further, amino acid additions may involve the fusion of a Cpn10 polypeptide or fragment thereof with a second polypeptide or peptide, such as a polyhistidine tag, maltose binding protein fusion, glutathione S transferase fusion, green fluorescent protein fusion, or the addition of an epitope tag such as FLAG, c-myc or hexahistidine tag. The Cpn10 polypeptide may or may not include the initiating methionine at the N terminus. For example, human Cpn10 may comprise at the N-terminus an additional GSM tripeptide moiety (SEQ ID No: 12; see for example WO 95/15338, the disclosure of which is incorporated herein by reference), an additional alanine (A; SEQ ID No. 3) or an additional glycine (G; SEQ ID No: 104). The present invention also contemplates the use of polynucleotides encoding such modified forms of Cpn10. In the case of Cpn10 polypeptides of the invention based on, or substantially derived from human Cpn10, such polypeptides typically comprise the N-terminal sequence MAGQAFRKFL, optionally including one or more modifications as described above. The term "variant" as used herein refers to substantially similar sequences. Generally, polypeptide sequence variants possess qualitative biological activity in common. Further, these polypeptide sequence variants may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity. Also included within the meaning of the term "variant" are homologues of polypeptides of the invention. A homologue is typically a polypeptide from a different species but sharing substantially the same biological function or activity as the corresponding polypeptide disclosed herein.
Further, the term "variant" also includes analogues of the polypeptides of the invention, wherein the term "analogue" means a polypeptide which is a derivative of a polypeptide of the invention, which derivative comprises addition, deletion, substitution of one or more amino acids, such that the polypeptide retains substantially the same function.
The present invention also contemplates fragments of the polypeptides disclosed herein. The term "fragment" refers to a polypeptide molecule that encodes a constituent or is a constituent of a polypeptide of the invention or variant thereof. Typically the fragment possesses qualitative biological activity in common with the polypeptide of which it is a constituent. The peptide fragment may be between about 5 to about 150 amino acids in length, between about 5 to about 100 amino acids in length, between about 5 to about 50 amino acids in length, or between about 5 to about 25 amino acids in length. Alternatively, the peptide fragment may be between about 5 to about 15 amino acids in length.
Cpn10 polypeptides modified at the N- and/or C-terminus by the addition, deletion or substitution of one or more amino acid residues as described above also fall within the scope of the present invention.
Production of CpnW
In accordance with the present invention Cpn10 polypeptides may be produced using standard techniques of recombinant DNA and molecular biology that are well known to those skilled in the art. Guidance may be obtained, for example, from standard texts such as Sambrook et ai, Molecular Cloning : A Laboratory Manual, Cold Spring Harbor, New York, 1989 and Ausubel et ai, Current Protocols in Molecular Biology, Greene Publ. Assoc, and Wiley-lntersciences, 1992. Methods described in Morton et ai, 2000 {Immunol Cell Biol 78:603-607), Ryan et ai, 1995 (J Biol Chem 270:22037-22043) and Johnson et al., 2005 (J Biol Chem 280:4037-4047) are examples of suitable purification methods for Cpn10 polypeptides, although the skilled addressee will appreciate that the present invention is not limited by the method of purification or production used and any other method may be used to produce Cpn10 for use in accordance with the methods and compositions of the present invention.
Cpn10 polypeptides and peptide fragments for use in accordance with the present invention may be obtained using of standard recombinant nucleic acid techniques or may be synthesized, for example using conventional liquid or solid phase synthesis techniques. Cpn10 peptides may be produced by digestion of a polypeptide with one or more proteinases such as endoLys-C, endoArg- C, endoGlu-C and staphylococcus V8-protease. The digested peptide fragments can be purified by, for example, high performance liquid chromatographic (HPLC) techniques.
The purification of Cpn10 polypeptides of the invention may be scaled-up for large-scale production purposes. For example, as described herein the present inventors have developed a bioprocess for the production of large (gram) quantities of highly pure, clinical grade Cpn10 polypeptides.
Cpn10 polypeptides of the present invention, as well as fragments and variants thereof, may also be synthesised by standard methods of liquid or solid phase chemistry well known to those of ordinary skill in the art. For example such molecules may be synthesised following the solid phase chemistry procedures of Steward and Young (Steward, J. M. & Young, J. D., Solid Phase Peptide Synthesis. (2nd Edn.) Pierce Chemical Co., Illinois, USA (1984).
In general, such a synthesis method comprises the sequential addition of one or more amino acids or suitably protected amino acids to a growing peptide chain. Typically, either the amino or carboxyl group of the first amino acid is protected by a suitable protecting group. The protected amino acid is then either attached to an inert solid support or utilised in solution by adding the next amino acid in the sequence having the complimentary (amino or carboxyl) group suitably protected and under conditions suitable for forming the amide linkage. The protecting group is then removed from this newly added amino acid residue and the next (protected) amino acid is added, and so forth. After all the desired amino acids have been linked, any remaining protecting groups, and if necessary any solid support, is removed sequentially or concurrently to produce the final polypeptide.
Amino acid changes in Cpn10 polypeptides may be effected by techniques well known to those persons skilled in the relevant art. For example, amino acid changes may be effected by nucleotide replacement techniques which include the addition, deletion or substitution of nucleotides
(conservative and/or non-conservative), under the proviso that the proper reading frame is maintained. Exemplary techniques include random mutagenesis, site-directed mutagenesis, oligonucleotide-mediated or polynucleotide-mediated mutagenesis, deletion of selected region(s) through the use of existing or engineered restriction enzyme sites, and the polymerase chain reaction.
The generation of immunomodulatory activity by the Cpn10 polypeptides of the invention may involve the formation of heptamers of the Cpn10 polypeptides. Testing of immunomodulatory activity for the purposes of the present invention may be via any one of a number of techniques known to those of skill in the art. As exemplified herein immunomodulatory activity of Cpn10 polypeptides may be determined by measuring the ability of the polypeptide to modulate signalling from the Toll-like receptor TLR-3, for example using an NF-κB-luciferase reporter cell line, and typically in the presence of a TLR-3 agonist such as poly(l:C). Other TLRs such as TLR-7, 8 and 9 are also tested as described herein. Alternatively or in addition, immunomodulatory activity may be determined using other assays in vitro, ex vivo or in vivo, for example via measurement of the production of cytokines in cells such as peripheral blood mononuclear cells, competitive binding assay, a two- hybrid assay, an electrophoretic mobility shift (gel-shift) assay or a plate capture assay.
Polynucleotides
Embodiments of the present invention provide isolated polynucleotides encoding Cpn10 polypeptides as described above, and variants and fragments of such polynucleotides. Non-limiting examples of polynucleotides that are contemplated within the scope of the invention are represented herein as SEQ ID Nos. 11-12, 14-15, 17-18, 20-21, 23-24, 26-27, 29-30, 32-33, 35-36, 38-39, 41 -42, 44-45, 47-48, 50-51 , 53-54, 56-57 and 59-60.
As for polypeptides discussed above, the term "variant" as used herein refers to substantially similar sequences. Generally, polynucleotide sequence variants encode polypeptides which possess qualitative biological activity in common. Further, these polynucleotide sequence variants may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity. Also included within the meaning of the term "variant" are homologues of polynucleotides of the invention. A homologue is typically a polynucleotide from a different species but sharing substantially the same activity.
Fragments of polynucleotides of the invention are also contemplated. The term "fragment" refers to a nucleic acid molecule that encodes a constituent or is a constituent of a polynucleotide of the invention. Fragments of a polynucleotide, do not necessarily need to encode polypeptides which retain biological activity. Rather the fragment may, for example, be useful as a hybridization probe or PCR primer. The fragment may be derived from a polynucleotide of the invention or alternatively may be synthesized by some other means, for example chemical synthesis. Polynucleotides of the invention and fragments thereof may also be used in the production of antisense molecules using techniques known to those skilled in the art.
Accordingly, the present invention contemplates oligonucleotides and fragments based on the sequences of the polynucleotides of the invention for use as primers and probes. Oligonucleotides are short stretches of nucleotide residues suitable for use in nucleic acid amplification reactions such as PCR, typically being at least about 10 nucleotides to about 50 nucleotides in length, more typically about 15 to about 30 nucleotides in length. Probes are nucleotide sequences of variable length, for example between about 10 nucleotides and several thousand nucleotides, for use in detection of homologous sequences, typically by hybridization. The level of homology (sequence identity) between sequences will largely be determined by the stringency of hybridization conditions. In particular the nucleotide sequence used as a probe may hybridize to a homologue or other variant of a polynucleotide disclosed herein under conditions of low stringency, medium stringency or high stringency. Low stringency hybridization conditions may correspond to hybridization performed at 50°C in 2 x SSC. There are numerous conditions and factors, well known to those skilled in the art, which may be employed to alter the stringency of hybridization. For instance, the length and nature (DNA, RNA, base composition) of the nucleic acid to be hybridized to a specified nucleic acid; concentration of salts and other components, such as the presence or absence of formamide, dextran sulfate, polyethylene glycol etc; and altering the temperature of the hybridization and/or washing steps. For example, a hybridization filter may be washed twice for 30 minutes in 2 X SSC, 0.5% SDS and at least 550C (low stringency), at least 600C (medium stringency), at least 65°C (medium/ high stringency), at least 70°C (high stringency) or at least 75°C (very high stringency).
In particular embodiments, polynucleotides of the invention may be cloned into a vector. The vector may be a plasmid vector, a viral vector, or any other suitable vehicle adapted for the insertion of foreign sequences, their introduction into eukaryotic cells and the expression of the introduced sequences. Typically the vector is a eukaryotic expression vector and may include expression control and processing sequences such as a promoter, an enhancer, ribosome binding sites, polyadenylation signals and transcription termination sequences.
Antibodies The present invention provides antibodies that selectively bind to the Cpn10 polypeptides of the present invention, as well as fragments and analogues thereof. Suitable antibodies include, but are not limited to polyclonal, monoclonal, chimeric, humanised, single chain, Fab fragments, and an Fab expression library. Antibodies of the present invention may act as agonists or antagonists of Cpn10 polypeptides, or fragments or analogues thereof. Antibodies may be prepared from discrete regions or fragments of the Cpn10 polypeptides of the invention, in particular those involved in conferring immunomodulatory activity and/or partner or substrate binding. An antigenic Cpn10 polypeptide contains at least about 5, and preferably at least about 10, amino acids. Methods for the generation of suitable antibodies will be readily appreciated by those skilled in the art. For example, an anti-Cpn10 monoclonal antibody, typically containing Fab portions, may be prepared using the hybridoma technology described in Antibodies-A Laboratory Manual, Harlow and Lane, eds., Cold Spring Harbor Laboratory, N.Y. (1988).
In the preparation of monoclonal antibodies directed toward Cpn10 polypeptides of the invention, fragments or analogues thereof, any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used. These include the hybridoma technique originally developed by Kohler et al., Nature, 256:495-497 (1975), as well as the trioma technique, the human B-cell hybridoma technique [Kozbor et al., Immunology Today, 4:72 (1983)], and the EBV-hybridoma technique to produce human monoclonal antibodies [Cole et al., in Monoclonal Antibodies and Cancer Therapy, pp. 77-96, Alan R. Liss, Inc., (1985)]. Immortal, antibody-producing cell lines can be created by techniques other than fusion, such as direct transformation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus. See, e.g., M. Schreier etal., "Hybridoma Techniques" (1980); Hammerling et al., "Monoclonal Antibodies and T-cell Hybridomas" (1981); Kennett etal., "Monoclonal Antibodies" (1980). In summary, a means of producing a hybridoma from which the monoclonal antibody is produced, a myeloma or other self-perpetuating cell line is fused with lymphocytes obtained from the spleen of a mammal hyperimmunised with a recognition factor-binding portion thereof, or recognition factor, or an origin-specific DNA-binding portion thereof. Hybridomas producing a monoclonal antibody useful in practicing this invention are identified by their ability to immunoreact with the present recognition factor and their ability to inhibit specified transcriptional activity in target cells.
A monoclonal antibody useful in practicing the present invention can be produced by initiating a monoclonal hybridoma culture comprising a nutrient medium containing a hybridoma that secretes antibody molecules of the appropriate antigen specificity. The culture is maintained under conditions and for a time period sufficient for the hybridoma to secrete the antibody molecules into the medium. The antibody-containing medium is then collected. The antibody molecules can then be further isolated by well-known techniques.
Similarly, there are various procedures known in the art which may be used for the production of polyclonal antibodies to Cpn10 polypeptides of the invention, or fragments or analogues thereof. For the production of Cpn10 polyclonal antibody, various host animals can be immunized by injection with a Cpn10 polypeptide, or a fragment or analogue thereof, including but not limited to rabbits, mice, rats, sheep, goats, etc. Further, the Cpn10 polypeptide or fragment or analogue thereof can be conjugated to an immunogenic carrier, e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH). Also, various adjuvants may be used to increase the immunological response, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminium hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvυm.
Screening for the desired antibody can also be accomplished by a variety of techniques known in the art. Assays for immunospecific binding of antibodies may include, but are not limited to, radioimmunoassays, ELISAs (enzyme-linked immunosorbent assay), sandwich immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays, Western blots, precipitation reactions, agglutination assays, complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, and the like (see, for example, Ausubel etai, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York). Antibody binding may be detected by virtue of a detectable label on the primary anti-Cpn10 antibody. Alternatively, the anti-Cpn10 antibody may be detected by virtue of its binding with a secondary antibody or reagent which is appropriately labelled. A variety of methods are known in the art for detecting binding in an immunoassay and are within the scope of the present invention.
Antibodies of the present invention can be used in diagnostic methods and kits that are well known to those of ordinary skill in the art to detect qualitatively or quantify Cpn10 in a body fluid or tissue, or alternatively antibodies may be used in methods and compositions for the treatment of various diseases, disorders and conditions. The antibody (or fragment thereof) raised against a Cpn10 polypeptide of the invention or a fragment or analogue thereof has binding affinity for Cpn10. Preferably, the antibody (or fragment thereof) has binding affinity or avidity greater than about 105 M-1, more preferably greater than about 106 M"1, more preferably still greater than about 107 M-' and most preferably greater than about 108 M-1. In terms of obtaining a suitable amount of an antibody according to the present invention, one may manufacture the antibody(s) using batch fermentation with serum free medium. After fermentation the antibody may be purified via a multistep procedure incorporating chromatography and viral inactivation/removal steps. For instance, the antibody may be first separated by Protein A affinity chromatography and then treated with solvent/detergent to inactivate any lipid enveloped viruses. Further purification, typically by anion and cation exchange chromatography may be used to remove residual proteins, solvents/detergents and nucleic acids. The purified antibody may be further purified and formulated into 0.9% saline using gel filtration columns. The formulated bulk preparation may then be sterilised and viral filtered and dispensed.
Agonists and antagonists
Using the methods described above, an agent may be identified that is an agonist of a polypeptide of the invention or a variant or fragment thereof. Agents which are agonists enhance one or more of the biological activities of the polypeptide. Alternatively, the methods described above may identify an agent that is an antagonist of a polypeptide of the invention or a variant or fragment thereof. Agents which are antagonists retard one or more of the biological activities of the polypeptide. Agonists enhance one or more of the biological activities of a molecule, such as Cpn10 polypeptides as described herein, whilst antagonists retard one or more of the biological activities of the polypeptides.
Such potential modulators of the activity of the polypeptides of the invention may be generated for screening by the above methods by a number of techniques known to those skilled in the art. For example, methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy may be used to model the structure of polypeptide of the invention or a variant or fragment thereof, thus facilitating the design of potential modulating agents using computer-based modeling. Various forms of combinatorial chemistry may also be used to generate putative modulators. Using the screeing methods as described below, an agent may be identified that is an agonist or antagonist of a polypeptide of the invention or a variant or fragment thereof. Antibodies, low molecular weight peptides, nucleic acids and non-proteinaceous organic molecules are examples of such agents that may act as agonists or antagonists of a polypeptide of the invention or a variant or fragment thereof.
Screening
Compounds which bind, or otherwise interact with the polypeptides and polynucleotides of the invention, and specifically compounds which modulate their activity, may be identified by a variety of suitable methods. Non limiting methods include the two-hybrid method, co- immunoprecipitation, affinity purification, mass spectroscopy, tandem affinity purification, phage display, label transfer, DNA microarrays/gene coexpression and protein microarrays.
Cpn10 polypeptides of the invention and appropriate fragments and variants can be used in high-throughput screens to assay candidate compounds for the ability to bind to, or otherwise interact with Cpn10. These candidate compounds can be further screened against functional Cpn10 to determine the effect of the compound on Cpn10 activity. The polypeptides and polynucleotides of the present invention, and fragments and analogues thereof are useful for the screening and identification of compounds and agents that interact with these molecules. In particular, desirable compounds are those that modulate the activity of these polypeptides and polynucleotides. Such compounds may exert a modulatory effect by activating, stimulating, increasing, inhibiting or preventing expression or activity of the polypeptides and/or polynucleotides. Suitable compounds may exert their effect by virtue of either a direct (for example binding) or indirect interaction .As described herein, there are methods of screening for a compound that may modulate the activity of, or otherwise interact with, Cpn10 polypeptides of the invention. These compounds may be identified by a variety of suitable methods. Interaction and/or binding may be determined using standard competitive binding assays, such as gel-shift assays and plate bound assays described within, or two-hybrid assay systems.
For example, the two-hybrid assay is a yeast-based genetic assay system (Fields and Song, 1989) typically used for detecting protein-protein interactions. Briefly, this assay takes advantage of the multi-domain nature of transcriptional activators. For example, the DNA-binding domain of a known transcriptional activator may be fused to a Cpn10 polypeptide of the invention, or fragment or variant thereof, and the activation domain of the transcriptional activator fused to a candidate protein. Interaction between the candidate protein and the Cpn10 polypeptide , or fragment or variant thereof, will bring the DNA-binding and activation domains of the transcriptional activator into close proximity. Interaction can thus be detected by virtue of transcription of a specific reporter gene activated by the transcriptional activator.
Alternatively, affinity chromatography may be used to identify binding partners of Cpn10. For example, a Cpn10 polypeptide of the invention, or fragment or variant thereof, may be immobilised on a support (such as sepharose) and cell lysates passed over the column. Proteins binding to the immobilised Cpn10 polypeptide, fragment or variant can then be eluted from the column and identified. Initially such proteins may be identified by N-terminal amino acid sequencing for example.
In a modification of the above technique, a fusion protein may be generated by fusing a Cpn10 polypeptide, fragment or variant to a detectable tag, such as alkaline phosphatase, and using a modified form of immunoprecipitation as described by Flanagan and Leder (1990).
Methods for detecting compounds that modulate Cpn10 activity may involve combining a Cpn10 polypeptide with a candidate compound and a suitable labelled substrate and monitoring the effect of the compound on Cpn10 by changes in the substrate (may be determined as a function of time). Suitable labelled substrates include those labelled for colourimetric, radiometric, fluorimetric or fluorescent resonance energy transfer (FRET) based methods, for example.
For example, co-immunoprecipation may be used to to determine whether a candidate agent or plurality of candidate agents interacts or binds with polypeptide of the invention or a variant or 5 fragment thereof. Using this technique, cyanotoxic organisms, cyanobacteria and/or dinoflagellates may be lysed under nondenaturing conditions suitable for the preservation of protein-protein interactions. The resulting solution can then be incubated with an antibody specific for a polypeptide of the invention or a variant or fragment thereof and immunoprecipitated from the bulk solution, for example by capture with an antibody-binding protein attached to a solid support.
I0 lmmunoprecipitation of the polypeptide of the invention or a variant or fragment thereof by this method facilitates the co-immunoprecipation of an agent associated with that protein. The '. identification an associated agent can be established using a number of methods known in the art, including but not limited to SDS-PAGE, western blotting, and mass spectrometry.
Alternatively, the phage display method may be used to to determine whether a candidate ι5 agent or plurality of candidate agents interacts or binds with a polypeptide of the invention or a variant or fragment thereof. Phage display is a test to screen for protein interactions by integrating multiple genes from a gene bank into phage. Under this method, recombinant DNA techniques are used to express numerous genes as fusions with the coat protein of a bacteriophage such the peptide or protein product of each gene is displayed on the surface of the viral particle. A whole0 library of phage-displayed peptides or protein products of interest can be produced in this way. The resulting libraries of phage-displayed peptides or protein products may then be screened for the ability to bind a polypeptide of the invention or a variant or fragment thereof. DNA extracted from interacting phage contains the sequences of interacting proteins.
Alternatively, affinity chromatography may be used to to determine whether a candidate5 agent or plurality of candidate agents interacts or binds with a polypeptide of the invention or a variant or fragment thereof. For example, a polypeptide of the invention or a variant or fragment thereof, may be immobilised on a support (such as sepharose) and cell lysates passed over the column. Proteins binding to the immobilised polypeptide of the invention or a variant or fragment thereof, may then be eluted from the column and identified, for example by N-terminal amino acid0 sequencing.
The present invention also contemplates compounds which may exert their modulatory effect on polypeptides of the invention by altering expression of the polypeptide. In this case, such compounds may be identified by comparing the level of expression of the polypeptide in the presence of a candidate compound with the level of expression in the absence of the candidate compound.
In the context of antibodies, screening for the desired antibody can also be accomplished by a variety of techniques known in the art. Assays for immunospecific binding of antibodies may include, but are not limited to, radioimmunoassays, ELISAs (enzyme-linked immunosorbent assay), sandwich immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays, Western blots, precipitation reactions, agglutination assays, complement fixation assays, immunofluorescence assays, protein A assays, and
Immunoelectrophoresis assays, and the like (see, for example, Ausubel et al., Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York (1994)). Antibody binding may be detected by virtue of a detectable label on the primary antibody. Alternatively, the antibody may be detected by virtue of its binding with a secondary antibody or reagent which is appropriately labelled. A variety of methods are known in the art for detecting binding in an immunoassay and are included in the scope of the present invention. It will be appreciated that the methods described above are merely examples of the types of methods that may be utilised to identify agents that are capable of interacting with, or modulating the activity of polypeptides of the invention or variants or fragments thereof. Other suitable methods will be known by persons skilled in the art and are within the scope of this invention.
Compositions and routes of administration
Cpn10 polypeptides and polynucleotides of the invention may be useful as therapeutic agents. These molecules find use, for example, in treating or preventing a disease or condition in a subject, by administering a therapeutically effective amount of such a molecule to the subject. Typically such diseases and conditions are amenable to treatment by modulation of the immune response in the subject. By way of example, such diseases and conditions may include acute or chronic inflammatory diseases such as insulin dependent diabetes mellitus, systemic lupus erythematosis, Sjorgren's disease, Graves disease, multiple sclerosis, rheumatoid arthritis, chronic fatigue syndrome, Alzheimer's disease, asthma, allergy, multiple sclerosis, GVHD, artherosclerosis, inflammatory pain or an infectious disease. The infectious disease may result from a bacterial, viral, or fungal infection. Accordingly, pharmaceutically useful compositions comprising Cpn10 polypeptides and polynucleotides for use in treating or preventing diseases and conditions are contemplated. Agonists and antagonists of Cpn10 polypeptides of the invention, including anti-Cpn10 antibodies, may also be useful as therapeutic agents. Accordingly, the present invention also contemplates methods of treatment using such agonists and antagonists and pharmaceutical compositions comprising the same. In general, suitable compositions for use in accordance with the methods of the present invention may be prepared according to methods and procedures that are known to those of ordinary skill in the art and accordingly may include a pharmaceutically acceptable carrier, diluent and/or adjuvant.
Compositions may be administered by standard routes. In general, the compositions may be administered by the parenteral (e.g., intravenous, intraspinal, subcutaneous or intramuscular), oral or topical route. Administration may be systemic, regional or local. The particular route of administration to be used in any given circumstance will depend on a number of factors, including the nature of the condition to be treated, the severity and extent of the condition, the required dosage of the particular compound to be delivered and the potential side-effects of the compound. In general, suitable compositions may be prepared according to methods which are known to those of ordinary skill in the art and may include a pharmaceutically acceptable diluent, adjuvant and/or excipient. The diluents, adjuvants and excipients must be "acceptable" in terms of being compatible with the other ingredients of the composition, and not deleterious to the recipient thereof.
Examples of pharmaceutically acceptable carriers or diluents are demineralised or distilled water; saline solution; vegetable based oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil, sesame oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil, sesame oil, arachis oil or coconut oil; silicone oils, including polysiloxanes, such as methyl polysiloxane, phenyl polysiloxane and methylphenyl polysolpoxane; volatile silicones; mineral oils such as liquid paraffin, soft paraffin or squalane; cellulose derivatives such as methyl cellulose, ethyl cellulose, carboxymethylcellulose, sodium carboxymethylcellulose or hydroxypropylmethylcellulose; lower alkanols, for example ethanol or iso-propanol; lower aralkanols; lower polyalkylene glycols or lower alkylene glycols, for example polyethylene glycol, polypropylene glycol, ethylene glycol, propylene glycol, 1,3-butylene glycol or glycerin; fatty acid esters such as isopropyl palmitate, isopropyl myristate or ethyl oleate; polyvinylpyrridone; agar; carrageenan; gum tragacanth or gum acacia, and petroleum jelly. Typically, the carrier or carriers will form from 10% to 99.9% by weight of the compositions.
The compositions of the invention may be in a form suitable for administration by injection, in the form of a formulation suitable for oral ingestion (such as capsules, tablets, caplets, elixirs, for example), in the form of an ointment, cream or lotion suitable for topical administration, in a form suitable for delivery as an eye drop, in an aerosol form suitable for administration by inhalation, such as by intranasal inhalation or oral inhalation, in a form suitable for parenteral administration, that is, subcutaneous, intramuscular or intravenous injection.
For administration as an injectable solution or suspension, non-toxic parenterally acceptable diluents or carriers can include, Ringer's solution, isotonic saline, phosphate buffered saline, ethanol and 1,2 propylene glycol.
Some examples of suitable carriers, diluents, excipients and adjuvants for oral use include peanut oil, liquid paraffin, sodium carboxymethylcellulose, methylcellulose, sodium alginate, gum acacia, gum tragacanth, dextrose, sucrose, sorbitol, mannitol, gelatine and lecithin. In addition these oral formulations may contain suitable flavouring and colourings agents. When used in capsule form the capsules may be coated with compounds such as glyceryl monostearate or glyceryl distearate which delay disintegration.
Adjuvants typically include emollients, emulsifiers, thickening agents, preservatives, bactericides and buffering agents.
Solid forms for oral administration may contain binders acceptable in human and veterinary pharmaceutical practice, sweeteners, disintegrating agents, diluents, flavourings, coating agents, preservatives, lubricants and/or time delay agents. Suitable binders include gum acacia, gelatine, corn starch, gum tragacanth, sodium alginate, carboxymethylcellulose or polyethylene glycol. Suitable sweeteners include sucrose, lactose, glucose, aspartame or saccharine. Suitable disintegrating agents include corn starch, methylcellulose, polyvinylpyrrolidone, guar gum, xanthan gum, bentonite, alginic acid or agar. Suitable diluents include lactose, sorbitol, mannitol, dextrose, kaolin, cellulose, calcium carbonate, calcium silicate or dicalcium phosphate. Suitable flavouring agents include peppermint oil, oil of wintergreen, cherry, orange or raspberry flavouring. Suitable coating agents include polymers or copolymers of acrylic acid and/or methacrylic acid and/or their esters, waxes, fatty alcohols, zein, shellac or gluten. Suitable preservatives include sodium benzoate, vitamin E, alpha-tocopherol, ascorbic acid, methyl paraben, propyl paraben or sodium bisulphite. Suitable lubricants include magnesium stearate, stearic acid, sodium oleate, sodium chloride or talc. Suitable time delay agents include glyceryl monostearate or glyceryl distearate.
Liquid forms for oral administration may contain, in addition to the above agents, a liquid carrier. Suitable liquid carriers include water, oils such as olive oil, peanut oil, sesame oil, sunflower oil, safflower oil, arachis oil, coconut oil, liquid paraffin, ethylene glycol, propylene glycol, polyethylene glycol, ethanol, propanol, isopropanol, glycerol, fatty alcohols, triglycerides or mixtures thereof.
Suspensions for oral administration may further comprise dispersing agents and/or suspending agents. Suitable suspending agents include sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethyl-cellulose, poly-vinyl-pyrrolidone, sodium alginate or acetyl alcohol. Suitable dispersing agents include lecithin, polyoxyethylene esters of fatty acids such as stearic acid, polyoxyethylene sorbitol mono- or di-oleate, -stearate or -laurate, polyoxyethylene sorbitan mono- or di-oleate, -stearate or -laurate and the like.
The emulsions for oral administration may further comprise one or more emulsifying agents. Suitable emulsifying agents include dispersing agents as exemplified above or natural gums such as guar gum, gum acacia or gum tragacanth.
Methods for preparing parenterally administrable compositions are apparent to those skilled in the art, and are described in more detail in, for example, Remington's Pharmaceutical Science, 15th ed., Mack Publishing Company, Easton, Pa., hereby incorporated by reference herein. The topical formulations of the present invention, comprise an active ingredient together with one or more acceptable carriers, and optionally any other therapeutic ingredients. Formulations suitable for topical administration include liquid or semi-liquid preparations suitable for penetration through the skin to the site of where treatment is required, such as liniments, lotions, creams, ointments or pastes, and drops suitable for administration to the eye, ear or nose. Drops according to the present invention may comprise sterile aqueous or oily solutions or suspensions. These may be prepared by dissolving the active ingredient in an aqueous solution of a bactericidal and/or fungicidal agent and/or any other suitable preservative, and optionally including a surface active agent. The resulting solution may then be clarified by filtration, transferred to a suitable container and sterilised. Sterilisation may be achieved by: autoclaving or maintaining at 9O0C-IOO0C for half an hour, or by filtration, followed by transfer to a container by an aseptic technique. Examples of bactericidal and fungicidal agents suitable for inclusion in the drops are phenylmercuric nitrate or acetate (0.002%), benzalkonium chloride (0.01%) and chlorhexidine acetate (0.01%). Suitable solvents for the preparation of an oily solution include glycerol, diluted alcohol and propylene glycol. Lotions according to the present invention include those suitable for application to the skin or eye. An eye lotion may comprise a sterile aqueous solution optionally containing a bactericide and may be prepared by methods similar to those described above in relation to the preparation of drops. Lotions or liniments for application to the skin may also include an agent to hasten drying and to cool the skin, such as an alcohol or acetone, and/or a moisturiser such as glycerol, or oil such as castor oil or arachis oil.
Creams, ointments or pastes according to the present invention are semi-solid formulations of the active ingredient for external application. They may be made by mixing the active ingredient in finely-divided or powdered form, alone or in solution or suspension in an aqueous or non-aqueous fluid, with a greasy or non-greasy basis. The basis may comprise hydrocarbons such as hard, soft or liquid paraffin, glycerol, beeswax, a metallic soap; a mucilage; an oil of natural origin such as almond, corn, arachis, castor or olive oil; wool fat or its derivatives, or a fatty acid such as stearic or oleic acid together with an alcohol such as propylene glycol or macrogols.
The composition may incorporate any suitable surfactant such as an anionic, cationic or non- ionic surfactant such as sorbitan esters or polyoxyethylene derivatives thereof. Suspending agents such as natural gums, cellulose derivatives or inorganic materials such as silicaceous silicas, and other ingredients such as lanolin, may also be included.
The compositions may also be administered in the form of liposomes. Liposomes are generally derived from phospholipids or other lipid substances, and are formed by mono- or multilamellar hydrated liquid crystals that are dispersed in an aqueous medium. Any non-toxic, physiologically acceptable and metabolisable lipid capable of forming liposomes can be used. The compositions in liposome form may contain stabilisers, preservatives, excipients and the like. The preferred lipids are the phospholipids and the phosphatidyl cholines (lecithins), both natural and synthetic. Methods to form liposomes are known in the art, and in relation to this specific reference is made to: Prescott, Ed., Methods in Cell Biology, Volume XIV, Academic Press, New York, N.Y. (1976), p. 33 el seq., the contents of which is incorporated herein by reference.
The compositions may be conjugated to an array of polyethylene glycol (PEG) derivatives. The addition of PEG to proteins (PEGylation) is a well established method for decreasing the plasma clearance rates of proteins, thereby increasing their efficacy (Nucci el al., 1991, Adv. Drug Del. Rev. 6:133). Additional benefits of PEGylation may include, greater stability of proteins, decreased immunogenicity, enhanced solubility and decreased susceptibility to proteolysis (Sheffield W. 2001, Curr Drug Targets Cardiovasc Haematol Disord. 1:1-22). PEG molecules contain the basic repeating structure of -(OCH3CH2)n-OH and are classified into groups according to their molecular weight. PEG derivatives are conjugated to proteins to increase their hydrodynamic radius and in general, their increase in half-life is directly related to the size of the PEG chain attached (Sheffield W.2001 , Curr Drug Targets Cardiovasc Haematol Disord. 1 : 1 -22).
The compositions may also be administered in the form of microparticles. Biodegradable microparticles formed from polylactide (PLA), polylactide-co-glycolide (PLGA), and epsilon- caprolactone (ε-caprolactone) have been extensively used as drug carriers to increase plasma half life and thereby prolong efficacy (R. Kumar, M., 2000, J Pharm Pharmaceut ScL 3(2) 234-258). Microparticles have been formulated for the delivery of a range of drug candidates including vaccines, antibiotics, and DNA. Moreover, these formulations have been developed for various delivery routes including parenteral subcutaneous injection, intravenous injection and inhalation.
The compositions may incorporate a controlled release matrix that is composed of sucrose acetate isobutyrate (SAIB) and organic solvent or organic solvents mixture. Polymer additives may be added to the vehicle as a release modifier to further increase the viscosity and slow down the release rate. SAIB is a well known food additive. It is a very hydrophobic, fully esterified sucrose derivative, at a nominal ratio of six isobutyrate to two acetate groups. As a mixed ester, SAIB does not crystallize but exists as a clear viscous liquid. Mixing SAIB with a pharmaceutically accepted organic solvent such as ethanol or benzyl alcohol decreases the viscosity of the mixture sufficiently to allow for injection. An active pharmaceutical ingredient may be added to the SAIB delivery vehicle to form SAIB solution or suspension formulations. When the formulation is injected subcutaneously, the solvent diffuses from the matrix allowing the SAIB-drug or SAIB-drug-polymer mixtures to set up as an in situ forming depot.
For the purposes of the present invention molecules and agents may be administered to subjects as compositions either therapeutically or preventively. In a therapeutic application, compositions are administered to a patient already suffering from a disease, in an amount sufficient to cure or at least partially arrest the disease and its complications. The composition should provide a quantity of the molecule or agent sufficient to effectively treat the patient.
Embodiments of the invention also contemplate the administration of a polynucleotide encoding Cpn10. In such situations the polynucleotide is typically operably linked to a promoter such that the appropriate polypeptide sequence is produced following administration of the polynucleotide to the subject. The polynucleotide may be administered to subjects in a vector. The vector may be a plasmid vector, a viral vector, or any other suitable vehicle adapted for the insertion of foreign sequences, their introduction into eukaryotic cells and the expression of the introduced sequences. Typically the vector is a eukaryotic expression vector and may include expression control and processing sequences such as a promoter, an enhancer, ribosome binding sites, polyadenylation signals and transcription termination sequences. The nucleic acid construct to be administered may comprise naked DNA or may be in the form of a composition, together with one or more pharmaceutically acceptable carriers. Those skilled in the art will appreciate that in accordance with the methods of the present invention Cpn10 polypeptides of the invention may be administered alone or in conjunction with one or more additional agents. For example, a Cpn10 polypeptide of the invention may be administered together with one or more agonists capable of stimulating a TLR receptor such as TLR-3. Additionally, the present invention contemplates combination therapy using Cpn10 polypeptides of the invention in conjunction with other therapeutic approaches to the treatment of diseases and disorders. For example, Cpn10 polypeptides may be useful in the treatment of viral diseases which are responsive to therapy with Type I interferons such as IFNβ or IFN1β and Cpn10 polypeptides of the invention may be used in conjunction with IFNβ in the treatment of autoimmune diseases such as multiple sclerosis. For such combination therapies, each component of the combination therapy may be administered at the same time, or sequentially in any order, or at different times, so as to provide the desired effect. Alternatively, the components may be formulated together in a single dosage unit as a combination product. When administered separately, it may be preferred for the components to be administered by the same route of administration, although it is not necessary for this to be so.
Dosages
The therapeutically effective dose level for any particular patient will depend upon a variety of factors including: the disorder being treated and the severity of the disorder; activity of the molecule or agent employed; the composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration; the route of administration; the rate of sequestration of the molecule or agent; the duration of the treatment; drugs used in combination or coincidental with the treatment, together with other related factors well known in medicine. One skilled in the art would be able, by routine experimentation, to determine an effective, non-toxic amount of agent or compound which would be required to treat applicable diseases and conditions.
Generally, an effective dosage is expected to be in the range of about 0.0001 mg to about IOOOmg per kg body weight per 24 hours; typically, about 0.001 mg to about 750mg per kg body weight per 24 hours; about 0.01 mg to about 500mg per kg body weight per 24 hours; about 0.1 mg to about 500mg per kg body weight per 24 hours; about 0.1 mg to about 250mg per kg body weight per 24 hours; about 1.Omg to about 250mg per kg body weight per 24 hours. More typically, an effective dose range is expected to be in the range about 1.0mg to about 200mg per kg body weight per 24 hours; about 1.0mg to about 100mg per kg body weight per 24 hours; about 1.0mg to about 50mg per kg body weight per 24 hours; about 1.0mg to about 25mg per kg body weight per 24 hours; about 5.0mg to about 50mg per kg body weight per 24 hours; about 5.0mg to about 20mg per kg body weight per 24 hours; about 5.0mg to about 15mg per kg body weight per 24 hours.
Alternatively, an effective dosage may be up to about 500mg/m2. Generally, an effective dosage is expected to be in the range of about 25 to about 500mg/m2, preferably about 25 to about 350mg/m2, more preferably about 25 to about 300mg/m2, still more preferably about 25 to about 250mg/m2, even more preferably about 50 to about 250mg/m2, and still even more preferably about 75 to about 150mg/m2.
Typically, in therapeutic applications, the treatment would be for the duration of the disease state. Further, it will be apparent to one of ordinary skill in the art that the optimal quantity and spacing of individual dosages will be determined by the nature and extent of the disease state being treated, the form, route and site of administration, and the nature of the particular individual being treated. Also, such optimum conditions can be determined by conventional techniques. It will also be apparent to one of ordinary skill in the art that the optimal course of treatment, such as, the number of doses of the composition given per day for a defined number of days, can be ascertained by those skilled in the art using conventional course of treatment determination tests.
The present invention will now be described with reference to specific examples, which should not be construed, in any way, as limiting the scope of the invention.
Examples
Example 1: Production of Cpn10 polypeptides
To further define the production process of Cpn10 polypeptides of the invention, the following non-limiting example is provided.
Firstly, a heat-inducible expression plasmid encoding human Cpn10 with an additional was transformed into the E. coli strain XL1-Blue (Stratagene), and a master cell bank was established from a single selected clone.
Cpn10 was then produced in E. coli essentially as described by Ryan el al. (1995, J Biol
Chem 270: 22037-22043). In addition, the material that did not bind Macro-Prep High Q (BioRad) was further purified by S-Sepharose and then Gel-Filtration (Superdex 200, Amersham Biosciences). Purified Cpn10 in a 50 mM Tris-HCI (pH 7.6) and 150 mM NaCI buffer, was filtered through an Acrodisc with a 0.2 mm Mustang E membrane according to the manufacturer's instructions (Pall Corporation, Ann Arbor, Ml. Cat No. MSTG5E3) to remove residual endotoxins and was stored at -7O0C. The purity of Cpn10, such as Ala-Cpn10, X-Cpn10, Ala-Cpn10-Y75K, X-
Cpn10-Y75K, Ala-Cpn10-Y75R and Ala-Cpn10-E34Q,Y75K, for example, was determined to be >99% by Coomassie brilliant staining on SDS-PAGE as shown in Figure 3. Aliquots were thawed once prior to use.
LPS contamination of Cpn10 was determined by the Limulus Amebocyte Lysate assay (BioWhittaker, Walkersville, MD) to be <0.03 EU/mg of purified Cpn10 protein. The authenticity of Cpn10 polypeptides obtained from the production process as described above was assessed on a batch by batch basis by mass spectrometry. Example 2: Molecular Chaperone activities of CprϊlO proteins
To examine the importance of the various amino acid residues, their potential charge, and the location of these residues in relation to chaperone activity, the inventors prepared various Cpn10 polypeptides which include one or more mutations such as Y75K, Y75R, Y75H, Y75D, Y75Q, (E74K,Y75E), (Y75G.G76K), Y75GK, D94K, D94N, E34Q or any combination thereof. Some these Cpn10 polypeptides have an extra N-terminal Alanine (Ala) residue (e.g. Ala-Cpn10-Y75K) and/or partially or substantially lack the N-terminus, mobile loop and/or the roof loop (e.g. Cpn 10- ΔNterm-Y75K, X-CpM 0-Δml-Y75K and Cpn10-β-barrel-Y75K).
The ability of these Cpn 10 polypeptides to act as a molecular chaperones and fold proteins in conjunction with E.coli GroEL was determined by assaying for rhodanese refolding in vitro utilising a method adapted from Weber F. and Hayer-Hartl M.K. (Chaperonin Protocols, Ed Schneider C, Humana Press Inc. , 2000, p117-126).
Native bovine rhodanese (30 μM, SIGMA) was denatured in 20 mM MOPS-KOH (pH7.5), 100 mM KCI and 20 mM MgCk (buffer A) containing 5M Guanidine HCI and 8 mM DTT then subsequently diluted (75-fold) from denaturant into buffer A containing GroEL (400 nM), such that the final concentration of rhodanese was 400 nM. GroEL rapidly and stably binds denatured rhodanese (D-Rho) whereas in buffer alone, D-Rho mis-folds and aggregates (ie inefficient spontaneous refolding). The addition of Cpn 10 and ATP (20.1 mM) to preformed, stable complexes of GroEL-bound rhodanese permits efficient refolding to proceed. In the absence of Cpn10, the addition of ATP causes D-Rho to cycle on and off GroEL in a folding incompetent manner leading eventually to misfolding and aggregation (this reaction serves as a suitable assay blank). Each folding reaction has a total volume of 290 μL, at specific time points (ie 0, 15, 30, 45, 60, 75, 90 mins) 30μL aliquots are removed and combined with 70μL of rhodanese activity assay mixture (57.1 mM KH2PO4 (pH7.5), 71.4 mM EDTA, 71.4 mM Na thiosulfate and 71.4 mM KCN) for 6 min. Prior to the initiation of refolding reactions with ATP, a 30 μL aliquot is taken as a T=O min of refolding time point. EDTA within the rhodanese activity assay mixture chelates Mg2+ ions, which prevents GroEL binding ATP, the result is an immediate stopping of the folding reaction. Subsequently, rhodanese activity is stopped after 6 min by the addition of 50 μL of 15% (v/v) formaldehyde (final concentration 5% v/v). Rhodanese catalyses the formation of thiocyanide ('Rhodanid') from thiosulfate and cyanide.
Thiocyanide is easily detected colourimetrically (Absorbance 450nm) by the formation of its red iron complex in the presence of Ferric Nitrate. Rhodanese activity measurements (150 μL) are developed by the addition of 150 μL of Ferric Nitrate reagent (164.5 mM ferric nitrate and 9.2 % v/v nitric acid). Rhodanese activity measurements are read at A450nm in 96 well microplates. A typical rhodanese folding reaction follow an exponential incline in rhodanese activity (ie folded rhodanese) with time to a maximum yield of folded rhodanese. At constant amounts of GroEL (40OnM) and rhodanese (40OnM), a linear relationship is observed (between rhodanese activity and time) with increasing amounts of Cpn10 until an equal molar concentration of Cpn10 (7mer) to GroEL (14mer) is reached (ie 400 nM). At concentrations of Cpn10 above 400 nM, the increase in rhodanese activity rapidly reaches a maximum. The assay consists of five standards (in duplicate) and test samples (in duplicate). The concentrations of Cpn10 standards are 0 nM, 140 nM, 250 nM, 280 nM and 350 nM. Rhodanese activity (ie Cpn10 activity) measurements from the 30, 45, 60, 75 and 90 min time points are averaged. The OnM Cpn10 standard serves as a suitable measurement of the assays' background activity; therefore the absorbance value for the OnM Cpn10 standard is subtracted from all other calculated absorbance values (or activity values). Following background correction, the absorbance value for the 280 nM Cpn10 standard is nominated as 100% activity and all other absorbance values are converted to a relative % activity based on the 100% standard. Outlier data points are removed by comparison of duplicate measurements, >30% deviation between duplicates is considered unacceptable. Utilizing the acceptable data, a linear calibration curve is generated with five standard concentrations 0 nM CpMO (0 % Activity), 140 nM Cpn10 (50 % Activity), 250 nM Cpn10 (89.3 % Activity), 280 nM Cpn10 (100 % Activity) and 350 nM Cpn10 (125 % Activity). Rhodanese activity (e,g, Ala-Cpn10 activity) is plotted against Ala-Cpn10 concentration. For correction of assay bias, the percentage activity values from the test samples are recalculated using the equation generated from the linear calibration curve.
Concentrations of chaperonins are calculated using the oligomeric molecular weights (MW) of the proteins while rhodanese is calculated using the monomeric MW; e.g. E. coli GroEL 14 mer (SwissProt P0A6F5) = 800,766.4 g/mol, Human AIa-CpMO 7 mer (SwissProt P61604) = 76,100.5 g/mol, Human X-CpMO- Y75K 7 mer = 75,358.5 g/mol, Human AIa-CpM 0-Y75K 7 mer = 75,855.5 g/mol and Bovine rhodanese 1 mer (SwisProt P00586) = 33,164.6 g/mol.
As shown in the table 1 below, the activities of the numerous CpMO proteins were determined from the Ala-Cpn10 standard curve linear equation. All reactions were done in duplicate. Table 1
Figure imgf000036_0001
Example 3: Cpn10 mutants bind to poly(l:C), CpG-ODNs and RNA
TLRs are expressed both extra- and intracellular^, those on the cell surface (TLR1, TLR2, TLR4, TLR5, TLR6, TLR10 and TLR11) generally recognize hydrophobic ligands while those in intracellular compartments (TLR3, TLR7, TLR8 and TLR9) generally recognize negatively charged nucleic acid based ligands (Akira et al. 2006, 124: 783-801 ).
As described herein, the inventors have shown that Ala-Cpn10 binds negatively charged nucleic acid based TLR ligands, these include poly(l:C) (TLR3 agonists) as shown in Figure 4, several classes of unmethylated single-stranded CpG-oligonucleotides (ODN) as shown in Figures
5 and 7 (human ODN-2216 class A, human ODN-2006 class B, human ODN-M362 class C; all TLR9 agonists) and E.coli K12 ssRNA (TLR7/8 ligand) as shown in Figure 6.
As described herein, the inventors have additionally shown that a number of mutants, for example X-Cpn10-Y75K, Ala-Cpn10-Y75K, Ala-Cpn10-Y75R, and Ala-Cpn10-D94K bind more tightly to poly(l:C) (Fig.4), CpG-ODNs (Fig. 5) and ssRNA (Fig.6) than Ala-Cpn10.
In relation to Fig 4, other mutants such as Ala-Cpn10-Y75R, Ala-Cpn10-Y75Q, AIa-CpMO- E74K.Y75E, AIa-CpM 0-Y75G.G76K, Ala-Cpn10-Y75GK, AIa-CpM 0-D94K, AIa-CpMO-
Y75K.D94K, AIa-CpM 0-D94N, AIa-CpM 0-E34Q, AIa-CpM 0-E34Q.Y75K, CpM0-ΔNterm-Y75K,
AIa-CpM 0-Δml-Y75K and Cpn10-β-barrel-Y75K also bind polyl:C more tightly than AIa-CpMO.
Furthermore, several mutants such as X-Cpn10-Y75K and AIa-CpM 0-Y75K bind so tightly toTLR3 agonist poly(l:C) that it cannot be fully released with 1M NaCI, unlike AIa-CpMO which is dissociated at 5OmM NaCI (Fig. 4). Intriguingly, at low NaCI concentrations X-CpMO binds the long polymers of poly(l:C) in manner that sequesters them from ethidium bromide intercalation (Fig. 4), possibly indicating that several CpMO heptamers bind a single poly(I.C) chain. Several mutants including X-CpM 0-Y75K and AIa-CpM 0-Y75K also sequester bound poly(l:C) from ethidium bromide intercalation at low salt concentrations but at ≥50 mM the binding site is opened enough for ethidium bromide intercalation without escape of the bound poly(l:C).
Unlike the interaction with poly(l:C), a stable complex of X-CpMO and AIa-CpMO with TLR9 agonists CpG-classes A, B and C was observed at physiological salt concentrations (~150mM) but to varying degrees could be dissociated at 50OmM NaCI (Fig. 5). Despite this naturally higher affinity for CpG-ODNs, the inventors observed that like the interaction with poly(l:C) a significantly stronger association was formed with X-CpMO- Y75K and AIa-CpM 0-Y75K (Fig. 4 and 5). In fact, CpG-classes A and B bound to either X-CpM 0-Y75K or Ala-Cpn10-Y75K were mostly resistant to 50OmM NaCI (Fig. 5). Additional mutants in Figure 5, such as AIa-CpM 0-Y75R, AIa-CpM 0-E74K.Y75E, Ala-CpM0-Y75GK, AIa-CpM 0-D94K, AIa-CpM 0-Y75K.D94K, AIa-CpMO- D94N, Ala-Cpn10-E34Q, Ala-Cpn10-E34Q,Y75K, Cpn10-ΔNterm-Y75K and Ala-Cpn10-Δml-Y75K also showed higher affinity to one or more CpG than Ala-Cpn10.
In regards to the TLR7 and TLR8 agonist E.coli K12 ssRNA, experiments also show a stronger association was formed with X-Cpn10-Y75K, Ala-Cpn10-Y75K, Ala-Cpn10-Y75R, AIa- Cpn10E74K,Y75E, Ala-Cpn10-Y75GK, AIa-CpM 0-D94K, Ala-Cpn10-Y75K,D94K, AIa-CpMO- D94N, Ala-CpM0E34Q, Ala-Cpn10-E34Q,Y75K, Cpn10-ΔNterm-Y75K and AIa-CpM 0-Δml-Y75K compared with Ala-Cpn10 (Fig. 6). At 15OmM NaCI Ala-Cpn10 and X-Cpn10 is completely removed from ssRNA but several mutants, including X-Cpn10-Y75K and Ala-Cpn10-Y75K for example remain firmly bound in the presence of 500 mM NaCI. In addition, high affinity binding was observed with Ala-Cpn10-E34Q (Figures 4 to 6) with all ligands studied demonstrating that the flexible mobile loop structures can indeed influence PRR ligand binding and that the introduction of multiple positive charges, supplied with AIa-CpMO- E34Q.Y75K, resulted in cumulative tigher binding to CpG-ODN classess-A\B\C when compared to AIa-CpM 0-E34Q and AIa-CpM 0-Y75K (Fig. 7).
Example 4: Quantitative analysis of Cpn10 binding to CpG oligonucleotides (ODNs)
To determine the amount of binding of the CpMO mutants to ODNs, the mutants were formulated at 10μg/μl in PBS pH7.2 (Invitrogen) and 50μg was adsorbed to triplicate wells of a 96 well plate 16 hr at 40C. Following the decanting of non-bound protein, the plate was blocked with 1% BSA and 5% sucrose in PBS pH7.2 for 2hr at 230C. 50μl of 3'-biotin labeled human ODN-2216 class-A, human ODN-2006 class-B, or human ODN-M362 class-C (TLR9 agonists) (Proligo/Sigma) formulated at 0.01 μg/μl in PBS pH 7.2 was added to each well and incubated for 2hr at 230C. Unbound ligand was removed with five PBS (pH7.2) + 0.05% Tween 20 washes. Bound CpG- ODNs were analysed with a Streptavidin-HRP and TMB detection system at A450nm. As shown in Figure 7, the CpMO mutants had a different binding affinity compared to AIa-
Cp10 and X-CpMO. Moreover, the majority of the CpMO mutants have an increased affinity, for ODNs, particularly, with CpG-A compared to AIa-CpMO and X-CpMO. In Figure 7 a quantitative analysis at physiological salt concentrations (~150mM) highlights the significantly stronger interaction of CpG-classes A, B and C with a number of mutants, for example X-CpM 0-Y75K, AIa- CpMO- Y75K, AIa-CpM 0-D94K, Ala-Cpn10-Y75R, AIa-CpM 0-E74K.Y75E, AIa-CpMO- Y75G.G76K, AIa-CpM 0-Y75GK, Ala-CpM0-Y75K,D94K, AIa-CpM 0-D94N, AIa-CpM 0-E34Q, AIa-CpMO- E34Q.Y75K, CpM0-ΔNterm-Y75K and AIa-CpM 0-Δml-Y75K compared to AIa-CpMO. Example 5: CprϊlO modulates CpG-B ODN-induced NFKB activity.
In order to establish whether high affinity binding of PRR ligands could be correlated with increased immunomodulatory activity, several cell based assays were developed to assess the abilities of various Cpn10 mutants to sequestor proinflammatory nucleic acids and thereby reduced the level of PRR signaling. Firstly, high affinity binders compared to Ala-Cpn10 and X-Cpn10 where incubated with CpG-ODN class B and the unbound PRR ligand was used to stimulate NFKB in mouse macrophages (RAW264 cells).
RAW264.7 (mouse macrophage) cells were stably transfected with an NFκB-luciferase reporter plasmid (pNIFty2-LUC; Invivogen). RAW264-pNIFty2-LUC cells were plated out and left to adhere overnight. 100μg of a Cpn10 construct or Formulation buffer control was mixed with 4 μg of CpG-B ODN-1826 (Invivogen) and passed through a centrifugal filter device YM10 (Amicon). The entire flow through volume was added to the RAW264-pNIFty2-LUC cells and incubated at 370C for 5 hours. Cells were washed and subsequently lysed with 100 μ I per well of CCLR 1X solution (Promega luciferase lysis buffer), mixed with luciferase substrate following the manufactures instructions and the luciferase counts measured.
Figure 8 shows NFKB activation levels (measured by luciferase) of TLR9 when CpG-B was mixed with either a Cpn10 construct or formulation buffer. The level of activation of TLR9 for AIa- Cpn10 was assigned the value of 100%. It can be seen from Figure 8 that isolated Cpn10 polypeptides comprising one or more amino acid substitutions, deletions and/or additions in mobile loop (which contains amino acid residue 34), C-terminus of the β-barrel (which contains amino acid residue 94) and/or other mutants within the lower rim region bind CpG-B, such as X-Cpn10-Y75K, Ala-Cpn10-Y75K, Ala-Cpn10-D94K, Ala-Cpn10-Y75R, Ala-Cpn10-E74K,Y75E, AIa-CpMO- Y75G.G76K, Ala-Cpn10-Y75GK, Ala-Cpn10-D94K, Ala-Cpn10-Y75K,D94K, Ala-Cpn10-D94N, AIa- Cpn10-E34Q, AIa-CpM 0-E34Q,Y75K, Cpn10-ΔNterm-Y75K and AIa-CpM 0-Δml-Y75K result in lower levels of activation of TLR9 than for Ala-Cpn 10.
Figure 8 shows a tight correlation between high affintiy binders and reduced NFKB levels compared to AIa-CpMO and X-CpMO. Likewise, mutants with comprimised affinities for PRR ligands, such as AIa-CpM 0-Y75D and Cpn10-βbarrel,Y75K, had an increased level of NFKB activation compared to AIa-CpMO and X-CpMO. In order to test the biological activities of high affinity binders on cells, CpMO variants were next assessed for their abilities to reduce proinflammatory NFKB activation (from HEK cells expressing TLR3) and IFN-α production (from human PBMCs) when stimulated with poly(l:C) and CpG-ODN class A, respectively. Example 6: Cpn10 mutants inhibit poly(l:C)-induced NFKB production through TLR-3 in HEK293 cells
HEK293 cells were transiently transfected with TLR3 and the pNIFTY-NFκB luciferase reporter gene. 24 hours post transfection cells were plated out into 24 well plates at 1 x 105 and left to adhere overnight. Cells were then stimulated for 18 hours with 0.1 ug poly(l:C) in the presence or absence of 100ug the Cpn10 mutants and 1OuI of SUPERase RNAse inhibitor (Ambion) as a competition assay (Fig. 9). PoIy(LC) and Cpn10 were mixed together at the required concentrations for 30 mins before being added to the cells. Three replicates of each condition were tested. 18 hours post stimulation cells were lysed and luciferase counts were measured. Luciferase counts were normalized to poly(l:C) alone, which was given the value of 100%.
When the cells were stimulated with poly(l:C), Ala-Cpn10 was able to reduce the level of luciferase (ie NFKB) by 22%. Several of the mutants, Ala-Cpn10-Y75K, X-Cpn10-Y75K, Ala-Cpn10-D94K, Ala-Cpn10-Y75G,G76K, AIa-CpM 0-Y75GK and AIa-CpM 0-E34Q,Y75K show significant modulation of Poly(l:C) induced TLR3, with AIa-CpM 0-Y75K reducing signalling by 53%, X-CpMO- Y75K reducing signalling by 71% and AIa-CpM 0-D94K reducing signalling by 82%, for example (fig. 9). This indicates that most of the CpMO mutants have the ability to modulate the immune system, particularly, when involving TLR3 signalling.
Example 7: CpMO effect on interferon-α production from PBMCs in the presence of CpG-A
To determine whether any of the CpMO mutants described herein have an effect on interferon-α production from PBMCs in the presence of CpG-A, human PBMC were isolated from buffy coats, counted and diluted to 3x106 cells/ml. 3ml of cells were plated in each well of a 6 well plate, together with 10ug CpMO and 0.25uM CpG-A (ODN2216, InvivoGen). Cells were incubated for 18hrs at 370C, 5% CO2, after which the supematants were removed and assayed for interferon- α levels using ELISA. As shown in Figure 10, CpMO mutants such as X-Cpn10-Y75K, AIa-CpM 0-Y75K, AIa-
Cpn10-Y75R, AIa-CpM 0-Y75GK, AIa-CpM 0-E34Q,Y75K, AIa-CpM 0-Y75G,G76K and AIa-CpMO- D94K had an effect on interferon production of PBMCs which is indicative that these mutants have an immunomodulatory effect on cells, particularly human cells.
In comparing the results of Figure 9 and 10, the inventors found that mutants such as AIa- Cpn10-Y75K, X-CpM0-Y75K, AIa-CpM 0-Y75G.G76K, AIa-CpM 0-Y75GK, AIa-CpM 0-D94K and AIa-CpM 0-E34Q.Y75K showed significantly increased activity compared to AIa-CpMO and X- CpMO (Figures 9 and 10). AIa-CpM 0-Y75R also had significantly increased activity in the CpG- ODN class A assay but wild-type activity in the poly(l:C) assay. Likewise, in both systems as represented in Figures 9 and 10, mutants with comprised (Ala-CpM0-Y75D and CpMO- βbarrel,Y75K) or similar (Ala-Cpn10-Y75H) binding characteristics to Ala-Cpn10 also displayed equivalent activities.
As discussed earlier, several high affintity binders, namely Ala-Cpn10-E74K,Y75E, AIa- Cpn10-E34Q, Cpn10-ΔNterm,Y75K and A!a-Cpn10-Δml,Y75K, displayed sub-optimal binding and interestingly these variants only have Ala-Cpn10-like activities in the reduction of NFKB activation (Fig. 9) and IFN-α production (Fig. 10).
Example 8: Panel of Mutants
In applying the above methods and tests, the inventors produced a number of Cpn10 polypeptides with various mutations to assess the importance of various amino acid residues (e.g. such as charge and positioning in the Cpn10 molecule) in their ability to have an increased binding to a PRR ligand, such as poly(l:C) and several classes of ODNs compared to such Cpn10 molecules as X-Cpn10 and Ala-Cpn10.
The inventors have substituted at least one of amino acid residue at position 12, 13, 21 to 26, 28 to 34, 36 to 38, 40 to 41, 52, 54, 56 to 62, 74 to 78, 81, 84, 86, 88 to 89, 92 to 94, 96 or any combination thereof of human Cpn10 with a positively charged or neutral residue according to the following table. The inventors have either replaced a neutral amino acid residue with a positively charged residue or replaced a negatively charged amino acid residue with a neutral or positively charged residue.
Figure imgf000041_0001
Figure imgf000042_0001
Figure imgf000043_0001
In addition to single mutations, the inventors have produced Cpn10 polypeptides with any combination of two or more of the above mutations such as double mutants (e.g. AIa-CpMO- E74K.Y75E, AIa-CpM 0-Y75G.G76K, AIa-CpM O- Y75K.D94K and AIa-CpM 0-E34Q.Y75K). The inventors have also constructed additional mutants which include any one or more mutations as listed above with the partial or substantial deletion of one or more loop regions of the CpMO molecule such as the mobile loop and the roof loop. For example, the inventors have constructed the following Cpn10 polypeptide mutants: Cpn10-ΔNterm,Y75K, X-Cpn10-Δml,Y75K and Cpn10-βbarrel,Y75K. It is contemplated herein that any combination of the above mutations that results in the creation of additional double mutants, triple mutants, and so on, are within the scope of the invention.
Example 9: Summary
The data thus far described reveals that the CpMO mutants as listed under Example 8 with high affinity for proinflammatory nucleic acid-based ligands of PRRs can be generated by adding positive or deleting negative residues under the CpMO dome or on flexible structures such as mobile loops and roof loops that can move under the dome. Specifically, the inventors have identified that AIa-CpM 0-Y75K, as well as many other CpMO mutants, had significantly improved affinity for poly(l:C), CpG-ODN classess-A\B\C and E.coli K12 ssRNA compared to AIa-CpMO (Figures 4 to 7) which could be attributed to not only increasing the net positive charge of the CpMO molecule through amino acid substitutions, deletions, and/or insertions but the location of the mutation and the size of the particular side chains of one or more of the amino acid residues comprising the mutation.
Furthermore, the inventors have found that high affinity binding could be achieved by introducing positive charge at several locations under the CpMO dome and that addition of multiple positive charges under the CpMO dome would provide cumulative tigher binding to proinflammatory nucleic acid-based ligands of PRRs.
The data described herein indicates that CpMO mutants with high affinity for proinflammatory nucleic acid-based ligands of PRRs can be generated by adding positive or deleting negative residues under the CpMO dome or on flexible structures (ie mobile loops and roof loops) that can move under the dome. The examples as laid out above show that several Cpn10 mutants as described herein have higher affinities for nucleic acid-based PRR ligands which is indicative of increased immunomodulatory activity in cell based assays of inflammation.

Claims

Claims:
1. An isolated CprϊlO polypeptide possessing an increased affinity for a PRR ligand compared to a wild-type Cpn10 polypeptide.
2. The polypeptide of claim 1, wherein said PRR ligand is selected from the group consisting of a Toll-like Receptor (TLR), Nucleotide-binding domain LRR-containing family (NLR), a RIG-l-like receptor (RLR), a DNA-dependent activator of IRF (DAI) and a C-type Lectin receptor (CLR).
3. The polypeptide of claim 2, wherein said TLR is selected from the group consisting of at least one of TLR3, TLR7, TLR8 or TLR9.
4. The polypeptide of any one of claims 1 to 3, wherein said polypeptide possesses a greater net positive charge compared to the wild-type Cpn10 polypeptide.
5. The polypeptide of any one of claims 1 to 4, wherein one or more wild-type Cpn10 polypeptides form a wild-type Cpn10 molecule.
6. The polypeptide of claim 5, wherein said polypeptide possesses at least one mutation under the dome of said wild-type Cpn10 molecule wherein said mutation is an amino acid substitution, addition or deletion.
7. The polypeptide of claim 6, wherein said mutation is the replacement of one or more amino acid residues with one or more positively charged residues.
8. The polypeptide of claim 6, wherein said mutation is the replacement of one or more amino acid residues with one or more neutral residues.
9. The polypeptide of claim 7, wherein said positively charged residue is selected from the group comprising an arginine (R), lysine (K) and histidine (H).
10. The polypeptide of claim 8, wherein said neutral residue is selected from the group comprising asparagine (N), glutamine (Q), serine (S), threonine (T), glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), proline (P), phenylalanine (F), tyrosine (Y), tryptophan (W), cysteine (C), methionine (M) and H (above pH 6.04).
11. The polypeptide of any one of claims 7 to 10, wherein said mutation under the dome is a mutation in either the mobile loop, or the roof loop, or at a position wherein a residue has free side chains within the inner surface of the Cpn10 molecule, or a combination thereof.
12. The polypeptide of any one of claims 6 to 11, wherein said polypeptide comprises a mutation at an amino acid position selected from the group consisting of position 12, 13, 21 to 26,
28 to 34, 36 to 38, 40 to 41 , 52, 54, 56 to 62, 74 to 78, 81 , 84, 86, 88 to 89, 92 to 94, and 96 of said wild-type Cpn10 molecule or a combination thereof.
13. The polypeptide of any one of claims 1 to 12, wherein said polypeptide comprises a mutation selected from the group consisting of F12K, D13K, A21K, A22K, E23K, T24K, V25K, T26K, G28K, G29K, I30K, M31K, L32K, P33K, E34K, S36K, Q37K, G38K, V40K, L41K, S52K, G54K, G56K, G57K, E58K, I59K, Q60K, P61K, V62K, E74K, Y75K, G76K, G77K, T78K, V81K, D84K, D86K, F88K, L89K, D92K, G93K, D94K, L96K, F12R, D13R, A21R, A22R, E23R, T24R, V25R, T26R, G28R, G29R, I30R, M31R, L32R, P33R, E34R, S36R, Q37R, G38R, V40R, L41R, s S52R, G54R, G56R, G57R, E58R, I59R, Q60R, P61R, V62R, E74R, Y75R, G76R, G77R, T78R, V81R, D84R, D86R, F88R, L89R, D92R, G93R, D94R, L96R, F12H, D13H, A21H, A22H, E23H, T24H, V25H, T26H, G28H, G29H, I30H, M31H, L32H, P33H, E34H, S36H, Q37H, G38H, V40H, L41H, S52H, G54H, G56H, G57H, E58H, I59H, Q60H, P61H, V62H, E74H, Y75H, G76H, G77H, T78H, V81H, D84H, D86H, F88H, L89H, D92H, G93H, D94H, L96H, D13N, E23Q, E34Q, E58Q,
I0 E74Q, D84N, D86N, D92N, D13G, E23G, E34G, E58G, E74G, D84G, D86G, D92G, D13A, E23A, E34A, E58A, E74A, D84A, D86A, D92A, D13V, E23V, E34V, E58V, E74V, D84V, D86V, D92V, D13L, E23L, E34L, E58L, E74L, D84L, D86L, D92L, D13I, E23I, E34I, E58I, E74I, D84I, D86I, D92I, D13P, E23P, E34P, E58P, E74P, D84P, D86P, D92P, D13F, E23F, E34F, E58F, E74F, D84F, D86F, D92F, D13Y, E23Y, E34Y, E58Y, E74Y, D84Y, D86Y, D92Y, D13W, E23W, E34W, is E58W, E74W, D84W, D86W, D92W, D13C, E23C, E34C, E58C, E74C, D84C, D86C, D92C, D13M, E23M, E34M, E58M, E74M, D84M, D86M, D92M, D13S, E23S, E34S, E58S, E74S, D84S, D86S, D92S, D13T, E23T, E34T, E58T, E74T, D84T, D86T, D92T, D13H, E23H, E34H, E58H, E74H, D84H, D86H, D92H or a combination thereof.
14. The polypeptide of any one of claims 1 to 13, wherein said polypeptide comprises a0 combination of two or more said mutations.
15. The polypeptide of claim 14, wherein said polypeptide comprises mutations selected from the group consisting of E74K.Y75E; Y75G.G76K; Y75K.D94K; D94N; Y75K.D94K and E34Q.Y75K.
16. The polypeptide of any one of claims 1 to 15, wherein said polypeptide lacks, or substantially lacks, the N-terminus, the mobile loop, the hairpin roof loop or a combination thereof.5
17. The polypeptide of claim 16, wherein said polypeptide is selected from the group consisting of Cpn10-ΔNterm-Y75K, X-Cpn10-Δml-Y75K and Cpn10-βbarrel-Y75K.
18. The polypeptide of any one of claims 1 to 17, wherein said polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 16,
19, 22, 25, 28,
31, 34, 37, 40, 43, 46, 49, 52, 55, 58 and 61-102. 0 19. The polypeptide of any one of claims 1 to 17, wherein said polypeptide comprises mutations selected from the group consisting of Y75K, Y75R, (Y75G,G76K), D94N, (Y75K.D94K),
Y75GK, D94K, (E74K.Y75E) and (E34Q.Y75K).
20. The polypeptide of claim 19, wherein said polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID Nos. 10, 13, 31 , 49, 52 and 55. 5
21. The polypeptide of claim 20, wherein said polypeptide is human Cpn10.
22. An isolated nucleic acid encoding a polypeptide according to any one of claims 1 to 21, wherein said nucleic acid comprises a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 17-18, 20-21, 23-24, 26-27, 29-30, 32-33, 35-36, 38-39, 41-42, 44-45, 47-48, 50-51, 53-54, 56-57 and 59-60.
5 23. The isolated nucleic acid of claim 22, wherein said nucleic acid comprises a nucleotide sequence selected from the group consisting of SEQ ID Nos. 11-12, 14-15, 32-33, 35-36, 50-51, 53-54 and 56-57.
24. An expression construct comprising a nucleic acid according to claim 22 or 23, wherein said construct is operably-linked to one or more regulatory sequences. o
25. A host cell expressing a polypeptide according to any one of claims 1 to 21, or comprising a nucleic acid according to claim 22 or 23 or an expression construct according to claim 24.
26. An antibody that selectively binds to a polypeptide according to any one of claims 1 to 21. s
27. A pharmaceutical composition comprising a polypeptide according to any one of claims 1 to 21, a nucleic acid according to claim 22 or 23, an expression construct according to claim 24 or an antibody according to claim 26.
28. A method of treating a subject, including the step of administering to said subject a therapeutically effective amount of a polypeptide according to any one of claims 1 to 21 or a nucleico acid according to claim 22 or 23.
29. The method of claim 28, wherein said treatment modulates the immune response in the subject, wherein said immune response is modulated via regulation of PRR signalling.
30. A method for treating or preventing a disease, disorder or condition in a subject, the method comprising administering to the subject an effective amount of a polypeptide according to5 any one of claims 1 to 21 or a nucleic acid according to claim 22 or 23.
31. The method of claim 30, wherein said disease, disorder or condition is selected from acute or chronic inflammatory diseases such as, insulin dependent diabetes mellitus, systemic lupus erythematosis, Sjorgren's disease, Graves disease, multiple sclerosis, rheumatoid arthritis, chronic fatigue syndrome, Alzheimer's disease, asthma, allergy, multiple sclerosis, GVHD,o artherosclerosis, inflammatory pain or an infectious disease.
32. A method for modulating PRR signalling in a subject, or in at least one cell, tissue or organ thereof, the method comprising administering a therapeutically effective amount of a polypeptide according to any one of claims 1 to 21 or a nucleic acid according to claim 22 or 23.
33. A method for modulating the production and/or secretion of one or more5 immunomodulators in a subject, or at least one cell, tissue or organ thereof, the method comprising administering a therapeutically effective amount of a polypeptide according to any one of claims 1 to 21 or a nucleic acid according to claim 22 or 23.
34. A method for inhibiting the production and/or secretion of one or more immunomodulators in a subject, or at least one cell, tissue or organ thereof, the method comprising administering an effective amount of a polypeptide according to any one of claims 1 to 21 or a nucleic acid according to claim 22 or 23.
35. The method of claim 33 or 34, wherein said immunomodulator is a pro-inflammatory cytokine or chemokine or an anti-inflammatory cytokine or chemokine, wherein said cytokine or chemokine is selected from TNF-α, IL-1 , IL-6, RANTES, IL-10, TGF-β or a type I interferon.
36. A method of identifying a compound that binds to a polypeptide according to any one of claims 1 to 21 , the method comprising the steps of:
(a) contacting a candidate compound with said polypeptide; and
(b) assaying for the formation of a complex between the candidate compound and said polypeptide.
37. The method of claim 36, wherein said assay is selected from the group comprising competitive binding assay, a two-hybrid assay, an electrophoretic mobility shift (gel-shift) assay and a plate capture assay.
38. A method of screening for a compound that modulates the activity of a polypeptide according to any one of claims 1 to 21 , the method comprising the steps of: (a) contacting said polypeptide with a candidate compound under conditions suitable to enable interaction of said candidate compound to said polypeptide; and (b) assaying for activity of said polypeptide.
39. A method of screening for a PRR ligand, the method comprising the steps of:
(a) contacting a polypeptide according to any one of claims 1 to 21 with a candidate PRR ligand compound under conditions suitable to enable interaction of said candidate compound to said polypeptide; and
(b) assaying for increased affinity of said compound with said polypeptide compared to wild type Cpn10; and/or
(c) assaying for decreased or increased PRR activation in the presence of the candidate PRR ligand compound and said polypeptide.
40. The polypeptide of any one of claims 1 to 21, wherein said polypeptide is a functional variant, derivative, homologue, analogue or fragment.
41. The polypeptide of any one of claims 1 to 21, wherein said wild-type Cpn10 molecule or polypeptide is either acetyl-Cpn10 (SEQ ID No. 1) or X-Cpn10 (SEQ ID No. 6).
PCT/AU2008/000520 2008-04-11 2008-04-11 Modified chaperonin 10 and prr signaling WO2009124333A1 (en)

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BRPI0911676A BRPI0911676A2 (en) 2008-04-11 2009-04-09 cpn10 isolated polypeptide, isolated nucleic acid, expression construct, host cell, antibody, pharmaceutical composition, method for treating or preventing a disease, method for modulating prr signaling, method for modulating the production and / or secretion of one or more immunomodulators, method for inhibiting production and / or secretion of one or more immunomodulators, method of identifying a compound that binds to a polypeptide, method for screening a coprote and a prr ligand and functional variant, derivative, homologue, analog or polypeptide fragment
MX2010011169A MX2010011169A (en) 2008-04-11 2009-04-09 Modified cpn10 and prr signalling.
KR1020107025213A KR20110005710A (en) 2008-04-11 2009-04-09 Modified cpn10 and prr signalling
CA2720617A CA2720617A1 (en) 2008-04-11 2009-04-09 Modified cpn10 and prr signalling
NZ588467A NZ588467A (en) 2008-04-11 2009-04-09 Modified chaperonin 10 (CPN10) polypeptides and pattern recognition receptor (PRR) signalling
AU2009235953A AU2009235953B2 (en) 2008-04-11 2009-04-09 Modified Cpn10 and PRR signalling

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WO2002083898A1 (en) * 2001-04-18 2002-10-24 Genset S.A. Full-length human cdnas encoding potentially secreted proteins
WO2005067959A1 (en) * 2004-01-16 2005-07-28 Cbio Limited Chaperonin 10 modulation of toll-like receptor-inducible cytokine and chemokine secretion
WO2007006095A2 (en) * 2005-07-11 2007-01-18 Cbio Limited Chaperonin 10-induced immunomodulation
WO2007025343A1 (en) * 2005-08-31 2007-03-08 Cbio Limited Modified chaperonin 10

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WO2002083898A1 (en) * 2001-04-18 2002-10-24 Genset S.A. Full-length human cdnas encoding potentially secreted proteins
WO2005067959A1 (en) * 2004-01-16 2005-07-28 Cbio Limited Chaperonin 10 modulation of toll-like receptor-inducible cytokine and chemokine secretion
WO2007006095A2 (en) * 2005-07-11 2007-01-18 Cbio Limited Chaperonin 10-induced immunomodulation
WO2007025343A1 (en) * 2005-08-31 2007-03-08 Cbio Limited Modified chaperonin 10

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